user32877: I am using an Arduino Leonardo (ATmega32U4) and need to use timer0 for PWM. Since by default in the wiring.c file the functions micros() and millis() use timer0, I decided that, since timer1 isn't being used, I could set up timer1 exactly how timer0 is set up for the micros() and millis() functions and modify their code so that it all uses timer1 instead of timer0.
I think in theory this should work. I read the datasheet and timer1, while being a 16-bit timer, can run in an 8-bit fast PWM mode (which is what timer0 is set up for). So I modified wiring.c to do as above: adjusted the prescaler to match the original for timer0 (f/64) and put timer1 into fast-pwm 8-bit mode.
I modified all functions in wiring.c that used any register from timer0 and changed them to use the corresponding registers in timer1.
However, the problem is that it seems like I did everything right, but when I try to run a simple program that calls Serial.println("hello world"), it is messed up. The output instead shows a repeated 'h' character to the serial console. I'm not really sure what's wrong and wondering if anyone can help.
Here is my re-written wiring.c file that essentially moves all the functionalities from timer0 to timer1:
#include "wiring_private.h"

// the prescaler is set so that timer0 ticks every 64 clock cycles,
// and the overflow handler is called every 256 ticks.
#define MICROSECONDS_PER_TIMER0_OVERFLOW (clockCyclesToMicroseconds(64 * 256))
// the whole number of milliseconds per timer0 overflow
#define MILLIS_INC (MICROSECONDS_PER_TIMER0_OVERFLOW / 1000)
// the fractional number of milliseconds per timer0 overflow. we shift right
// by three to fit these numbers into a byte. (for the clock speeds we care
// about - 8 and 16 MHz - this doesn't lose precision.)
#define FRACT_INC ((MICROSECONDS_PER_TIMER0_OVERFLOW % 1000) >> 3)
#define FRACT_MAX (1000 >> 3)

volatile unsigned long timer0_overflow_count = 0;
volatile unsigned long timer0_millis = 0;
static unsigned char timer0_fract = 0;

#if defined(__AVR_ATtiny24__) || defined(__AVR_ATtiny44__) || defined(__AVR_ATtiny84__)
ISR(TIM0_OVF_vect)
#else
/*************************** Modified wiring.c TIMER1 ISR ***********************/  
ISR(TIMER1_OVF_vect)
#endif
{
    // copy these to local variables so they can be stored in registers
    // (volatile variables must be read from memory on every access)
    unsigned long m = timer0_millis;
    unsigned char f = timer0_fract;

    m += MILLIS_INC;
    f += FRACT_INC;
    if (f >= FRACT_MAX) {
        f -= FRACT_MAX;
        m += 1;
    }
    timer0_fract = f;
    timer0_millis = m;
    timer0_overflow_count++;
}
/************************** End TIMER1 ISR **************************************/

unsigned long millis() {
    unsigned long m;
    uint8_t oldSREG = SREG;
    // disable interrupts while we read timer0_millis or we might get
    // an inconsistent value (e.g. in the middle of a write to timer0_millis)
    cli();
    m = timer0_millis;
    SREG = oldSREG;
    return m;
}

/************************ Modified micros() function ****************************/
unsigned long micros() {
    unsigned long m;
    uint8_t oldSREG = SREG, t;
    cli();
    m = timer0_overflow_count;
#if defined(TCNT1)
    t = TCNT1;
#else
    #error TIMER 1 not defined
#endif

#ifdef TIFR1
    if ((TIFR1 & _BV(TOV1)) && (t < 255))
        m++;
#else
    #error TIFR 1 not defined
#endif
    SREG = oldSREG;
    return ((m << 8) + t) * (64 / clockCyclesPerMicrosecond());
}
/************************ End micros() ******************************************/

void delay(unsigned long ms) {
    uint32_t start = micros();
    while (ms > 0) {
        yield();
        while ( ms > 0 && (micros() - start) >= 1000) {
            ms--;
            start += 1000;
        }
    }
}

/* Delay for the given number of microseconds.  Assumes a 1, 8, 12, 16, 20 or 24 MHz clock. */
void delayMicroseconds(unsigned int us) {
    // call = 4 cycles + 2 to 4 cycles to init us(2 for constant delay, 4 for variable)
    // calling avrlib's delay_us() function with low values (e.g. 1 or
    // 2 microseconds) gives delays longer than desired.
    //delay_us(us);
#if F_CPU >= 24000000L
    // for the 24 MHz clock for the aventurous ones, trying to overclock
    // zero delay fix
    if (!us) return; //  = 3 cycles, (4 when true)
    // the following loop takes a 1/6 of a microsecond (4 cycles)
    // per iteration, so execute it six times for each microsecond of
    // delay requested.
    us *= 6; // x6 us, = 7 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 22 (24) cycles above, remove 5, (5*4=20)
    // us is at least 6 so we can substract 5
    us -= 5; //=2 cycles

#elif F_CPU >= 20000000L
    // for the 20 MHz clock on rare Arduino boards
    // for a one-microsecond delay, simply return.  the overhead
    // of the function call takes 18 (20) cycles, which is 1us
    __asm__ __volatile__ (
        "nop" "\n\t"
        "nop" "\n\t"
        "nop" "\n\t"
        "nop"); //just waiting 4 cycles
    if (us <= 1) return; //  = 3 cycles, (4 when true)

    // the following loop takes a 1/5 of a microsecond (4 cycles)
    // per iteration, so execute it five times for each microsecond of
    // delay requested.
    us = (us << 2) + us; // x5 us, = 7 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 26 (28) cycles above, remove 7, (7*4=28)
    // us is at least 10 so we can substract 7
    us -= 7; // 2 cycles

#elif F_CPU >= 16000000L
    // for the 16 MHz clock on most Arduino boards
    // for a one-microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 1us
    if (us <= 1) return; //  = 3 cycles, (4 when true)
    // the following loop takes 1/4 of a microsecond (4 cycles)
    // per iteration, so execute it four times for each microsecond of
    // delay requested.
    us <<= 2; // x4 us, = 4 cycles

    // account for the time taken in the preceding commands.
    // we just burned 19 (21) cycles above, remove 5, (5*4=20)
    // us is at least 8 so we can subtract 5
    us -= 5; // = 2 cycles,
#elif F_CPU >= 12000000L
    // for the 12 MHz clock if somebody is working with USB

    // for a 1 microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 1.5us
    if (us <= 1) return; //  = 3 cycles, (4 when true)

    // the following loop takes 1/3 of a microsecond (4 cycles)
    // per iteration, so execute it three times for each microsecond of
    // delay requested.
    us = (us << 1) + us; // x3 us, = 5 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 20 (22) cycles above, remove 5, (5*4=20)
    // us is at least 6 so we can substract 5
    us -= 5; //2 cycles

#elif F_CPU >= 8000000L
    // for the 8 MHz internal clock

    // for a 1 and 2 microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 2us
    if (us <= 2) return; //  = 3 cycles, (4 when true)

    // the following loop takes 1/2 of a microsecond (4 cycles)
    // per iteration, so execute it twice for each microsecond of
    // delay requested.
    us <<= 1; //x2 us, = 2 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 17 (19) cycles above, remove 4, (4*4=16)
    // us is at least 6 so we can substract 4
    us -= 4; // = 2 cycles

#else
    // for the 1 MHz internal clock (default settings for common Atmega microcontrollers)

    // the overhead of the function calls is 14 (16) cycles
    if (us <= 16) return; //= 3 cycles, (4 when true)
    if (us <= 25) return; //= 3 cycles, (4 when true), (must be at least 25 if we want to substract 22)

    // compensate for the time taken by the preceeding and next commands (about 22 cycles)
    us -= 22; // = 2 cycles
    // the following loop takes 4 microseconds (4 cycles)
    // per iteration, so execute it us/4 times
    // us is at least 4, divided by 4 gives us 1 (no zero delay bug)
    us >>= 2; // us div 4, = 4 cycles
#endif
    // busy wait
    __asm__ __volatile__ (
        "1: sbiw %0,1" "\n\t" // 2 cycles
        "brne 1b" : "=w" (us) : "0" (us) // 2 cycles
    );
    // return = 4 cycles
}

void init() {
    // this needs to be called before setup() or some functions won't
    // work there
    sei();

    // on the ATmega168, timer 0 is also used for fast hardware pwm
    // (using phase-correct PWM would mean that timer 0 overflowed half as often
    // resulting in different millis() behavior on the ATmega8 and ATmega168)
#if defined(TCCR0A) && defined(WGM01)
    sbi(TCCR0A, WGM01);
    sbi(TCCR0A, WGM00);
#endif

    // set timer 0 prescale factor to 64
#if defined(__AVR_ATmega128__)
    // CPU specific: different values for the ATmega128
    sbi(TCCR0, CS02);
#elif defined(TCCR0) && defined(CS01) && defined(CS00)
    // this combination is for the standard atmega8
    sbi(TCCR0, CS01);
    sbi(TCCR0, CS00);
#elif defined(TCCR0B) && defined(CS01) && defined(CS00)
    // this combination is for the standard 168/328/1280/2560
    sbi(TCCR0B, CS01);
    sbi(TCCR0B, CS00);
#elif defined(TCCR0A) && defined(CS01) && defined(CS00)
    // this combination is for the __AVR_ATmega645__ series
    sbi(TCCR0A, CS01);
    sbi(TCCR0A, CS00);
#else
    #error Timer 0 prescale factor 64 not set correctly
#endif

    // enable timer 0 overflow interrupt
#if defined(TIMSK) && defined(TOIE0)
    sbi(TIMSK, TOIE0);
#elif defined(TIMSK0) && defined(TOIE0)
    sbi(TIMSK0, TOIE0);
#else
    #error  Timer 0 overflow interrupt not set correctly
#endif

    // timers 1 and 2 are used for phase-correct hardware pwm
    // this is better for motors as it ensures an even waveform
    // note, however, that fast pwm mode can achieve a frequency of up
    // 8 MHz (with a 16 MHz clock) at 50% duty cycle

/******************** Modified Code for Timer 1 *********************************/
#if defined(TCCR1B) && defined(CS11) && defined(WGM10)
    // set timer 1 prescale factor to 64
    sbi(TCCR1B, CS11);      
    sbi(TCCR1B, CS10);

    // put timer 1 in 8-bit fast pwm mode
    sbi(TCCR1B, WGM12);
    sbi(TCCR1A, WGM10);     

    // enable timer 1 overflow interrupt
    sbi(TIMSK1, TOIE1);
#endif
/********************* End Timer 1 **********************************************/

    // set timer 2 prescale factor to 64
#if defined(TCCR2) && defined(CS22)
    sbi(TCCR2, CS22);
#elif defined(TCCR2B) && defined(CS22)
    sbi(TCCR2B, CS22);
//#else
    // Timer 2 not finished (may not be present on this CPU)
#endif

    // configure timer 2 for phase correct pwm (8-bit)
#if defined(TCCR2) && defined(WGM20)
    sbi(TCCR2, WGM20);
#elif defined(TCCR2A) && defined(WGM20)
    sbi(TCCR2A, WGM20);
//#else
    // Timer 2 not finished (may not be present on this CPU)
#endif

/************** Modified Code for Timer 3 ***************************************/
#if defined(TCCR3B) && defined(CS31) && defined(WGM30)
    // set timer 3 prescale factor to 64
    sbi(TCCR3B, CS31);      
    sbi(TCCR3B, CS30);

    // put timer 3 in 8-bit fast pwm mode
    sbi(TCCR3B, WGM32);
    sbi(TCCR3A, WGM30);     

    // enable timer 3 overflow interrupt
    sbi(TIMSK3, TOIE3);
#endif
/************** End Timer 3 *****************************************************/

#if defined(TCCR4A) && defined(TCCR4B) && defined(TCCR4D) /* beginning of timer4 block for 32U4 and similar */
    sbi(TCCR4B, CS42);      // set timer4 prescale factor to 64
    sbi(TCCR4B, CS41);
    sbi(TCCR4B, CS40);
    sbi(TCCR4D, WGM40);     // put timer 4 in phase- and frequency-correct PWM mode 
    sbi(TCCR4A, PWM4A);     // enable PWM mode for comparator OCR4A
    sbi(TCCR4C, PWM4D);     // enable PWM mode for comparator OCR4D
#else /* beginning of timer4 block for ATMEGA1280 and ATMEGA2560 */
#if defined(TCCR4B) && defined(CS41) && defined(WGM40)
    sbi(TCCR4B, CS41);      // set timer 4 prescale factor to 64
    sbi(TCCR4B, CS40);
    sbi(TCCR4A, WGM40);     // put timer 4 in 8-bit phase correct pwm mode
#endif
#endif /* end timer4 block for ATMEGA1280/2560 and similar */   

#if defined(TCCR5B) && defined(CS51) && defined(WGM50)
    sbi(TCCR5B, CS51);      // set timer 5 prescale factor to 64
    sbi(TCCR5B, CS50);
    sbi(TCCR5A, WGM50);     // put timer 5 in 8-bit phase correct pwm mode
#endif

#if defined(ADCSRA)
    // set a2d prescaler so we are inside the desired 50-200 KHz range.
    #if F_CPU >= 16000000 // 16 MHz / 128 = 125 KHz
        sbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #elif F_CPU >= 8000000 // 8 MHz / 64 = 125 KHz
        sbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        cbi(ADCSRA, ADPS0);
    #elif F_CPU >= 4000000 // 4 MHz / 32 = 125 KHz
        sbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #elif F_CPU >= 2000000 // 2 MHz / 16 = 125 KHz
        sbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        cbi(ADCSRA, ADPS0);
    #elif F_CPU >= 1000000 // 1 MHz / 8 = 125 KHz
        cbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #else // 128 kHz / 2 = 64 KHz -> This is the closest you can get, the prescaler is 2
        cbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #endif
    // enable a2d conversions
    sbi(ADCSRA, ADEN);
#endif

    // the bootloader connects pins 0 and 1 to the USART; disconnect them
    // here so they can be used as normal digital i/o; they will be
    // reconnected in Serial.begin()
#if defined(UCSRB)
    UCSRB = 0;
#elif defined(UCSR0B)
    UCSR0B = 0;
#endif
}


user32879: Just for the record, I posted this question before I made an account by mistake, so that is why I cannot select best answer; BUT, I found the solution for anyone wondering.
I had the interrupt enabled for more than one timer (forgot to disable interrupts on the timer0 code). Once, i did that the code worked! I was able to move the millis, micros, delay, and delayMicros functions to the 16-bit timer 1!

32877: <p>I am using an Arduino Leonardo (ATmega32U4) and need to use timer0 for PWM. Since by default in the wiring.c file the functions <code>micros()</code> and <code>millis()</code> use timer0, I decided that, since timer1 isn't being used, I could set up timer1 exactly how timer0 is set up for the <code>micros()</code> and <code>millis()</code> functions and modify their code so that it all uses timer1 instead of timer0.</p>

<p>I think in theory this should work. I read the datasheet and timer1, while being a 16-bit timer, can run in an 8-bit fast PWM mode (which is what timer0 is set up for). So I modified wiring.c to do as above: adjusted the prescaler to match the original for timer0 (f/64) and put timer1 into fast-pwm 8-bit mode.</p>

<p>I modified all functions in wiring.c that used any register from timer0 and changed them to use the corresponding registers in timer1.</p>

<p>However, the problem is that it seems like I did everything right, but when I try to run a simple program that calls <code>Serial.println("hello world")</code>, it is messed up. The output instead shows a repeated 'h' character to the serial console. I'm not really sure what's wrong and wondering if anyone can help.</p>

<p>Here is my re-written wiring.c file that essentially moves all the functionalities from timer0 to timer1:</p>

<pre><code>#include "wiring_private.h"

// the prescaler is set so that timer0 ticks every 64 clock cycles,
// and the overflow handler is called every 256 ticks.
#define MICROSECONDS_PER_TIMER0_OVERFLOW (clockCyclesToMicroseconds(64 * 256))
// the whole number of milliseconds per timer0 overflow
#define MILLIS_INC (MICROSECONDS_PER_TIMER0_OVERFLOW / 1000)
// the fractional number of milliseconds per timer0 overflow. we shift right
// by three to fit these numbers into a byte. (for the clock speeds we care
// about - 8 and 16 MHz - this doesn't lose precision.)
#define FRACT_INC ((MICROSECONDS_PER_TIMER0_OVERFLOW % 1000) &gt;&gt; 3)
#define FRACT_MAX (1000 &gt;&gt; 3)

volatile unsigned long timer0_overflow_count = 0;
volatile unsigned long timer0_millis = 0;
static unsigned char timer0_fract = 0;

#if defined(__AVR_ATtiny24__) || defined(__AVR_ATtiny44__) || defined(__AVR_ATtiny84__)
ISR(TIM0_OVF_vect)
#else
/*************************** Modified wiring.c TIMER1 ISR ***********************/  
ISR(TIMER1_OVF_vect)
#endif
{
    // copy these to local variables so they can be stored in registers
    // (volatile variables must be read from memory on every access)
    unsigned long m = timer0_millis;
    unsigned char f = timer0_fract;

    m += MILLIS_INC;
    f += FRACT_INC;
    if (f &gt;= FRACT_MAX) {
        f -= FRACT_MAX;
        m += 1;
    }
    timer0_fract = f;
    timer0_millis = m;
    timer0_overflow_count++;
}
/************************** End TIMER1 ISR **************************************/

unsigned long millis() {
    unsigned long m;
    uint8_t oldSREG = SREG;
    // disable interrupts while we read timer0_millis or we might get
    // an inconsistent value (e.g. in the middle of a write to timer0_millis)
    cli();
    m = timer0_millis;
    SREG = oldSREG;
    return m;
}

/************************ Modified micros() function ****************************/
unsigned long micros() {
    unsigned long m;
    uint8_t oldSREG = SREG, t;
    cli();
    m = timer0_overflow_count;
#if defined(TCNT1)
    t = TCNT1;
#else
    #error TIMER 1 not defined
#endif

#ifdef TIFR1
    if ((TIFR1 &amp; _BV(TOV1)) &amp;&amp; (t &lt; 255))
        m++;
#else
    #error TIFR 1 not defined
#endif
    SREG = oldSREG;
    return ((m &lt;&lt; 8) + t) * (64 / clockCyclesPerMicrosecond());
}
/************************ End micros() ******************************************/

void delay(unsigned long ms) {
    uint32_t start = micros();
    while (ms &gt; 0) {
        yield();
        while ( ms &gt; 0 &amp;&amp; (micros() - start) &gt;= 1000) {
            ms--;
            start += 1000;
        }
    }
}

/* Delay for the given number of microseconds.  Assumes a 1, 8, 12, 16, 20 or 24 MHz clock. */
void delayMicroseconds(unsigned int us) {
    // call = 4 cycles + 2 to 4 cycles to init us(2 for constant delay, 4 for variable)
    // calling avrlib's delay_us() function with low values (e.g. 1 or
    // 2 microseconds) gives delays longer than desired.
    //delay_us(us);
#if F_CPU &gt;= 24000000L
    // for the 24 MHz clock for the aventurous ones, trying to overclock
    // zero delay fix
    if (!us) return; //  = 3 cycles, (4 when true)
    // the following loop takes a 1/6 of a microsecond (4 cycles)
    // per iteration, so execute it six times for each microsecond of
    // delay requested.
    us *= 6; // x6 us, = 7 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 22 (24) cycles above, remove 5, (5*4=20)
    // us is at least 6 so we can substract 5
    us -= 5; //=2 cycles

#elif F_CPU &gt;= 20000000L
    // for the 20 MHz clock on rare Arduino boards
    // for a one-microsecond delay, simply return.  the overhead
    // of the function call takes 18 (20) cycles, which is 1us
    __asm__ __volatile__ (
        "nop" "\n\t"
        "nop" "\n\t"
        "nop" "\n\t"
        "nop"); //just waiting 4 cycles
    if (us &lt;= 1) return; //  = 3 cycles, (4 when true)

    // the following loop takes a 1/5 of a microsecond (4 cycles)
    // per iteration, so execute it five times for each microsecond of
    // delay requested.
    us = (us &lt;&lt; 2) + us; // x5 us, = 7 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 26 (28) cycles above, remove 7, (7*4=28)
    // us is at least 10 so we can substract 7
    us -= 7; // 2 cycles

#elif F_CPU &gt;= 16000000L
    // for the 16 MHz clock on most Arduino boards
    // for a one-microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 1us
    if (us &lt;= 1) return; //  = 3 cycles, (4 when true)
    // the following loop takes 1/4 of a microsecond (4 cycles)
    // per iteration, so execute it four times for each microsecond of
    // delay requested.
    us &lt;&lt;= 2; // x4 us, = 4 cycles

    // account for the time taken in the preceding commands.
    // we just burned 19 (21) cycles above, remove 5, (5*4=20)
    // us is at least 8 so we can subtract 5
    us -= 5; // = 2 cycles,
#elif F_CPU &gt;= 12000000L
    // for the 12 MHz clock if somebody is working with USB

    // for a 1 microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 1.5us
    if (us &lt;= 1) return; //  = 3 cycles, (4 when true)

    // the following loop takes 1/3 of a microsecond (4 cycles)
    // per iteration, so execute it three times for each microsecond of
    // delay requested.
    us = (us &lt;&lt; 1) + us; // x3 us, = 5 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 20 (22) cycles above, remove 5, (5*4=20)
    // us is at least 6 so we can substract 5
    us -= 5; //2 cycles

#elif F_CPU &gt;= 8000000L
    // for the 8 MHz internal clock

    // for a 1 and 2 microsecond delay, simply return.  the overhead
    // of the function call takes 14 (16) cycles, which is 2us
    if (us &lt;= 2) return; //  = 3 cycles, (4 when true)

    // the following loop takes 1/2 of a microsecond (4 cycles)
    // per iteration, so execute it twice for each microsecond of
    // delay requested.
    us &lt;&lt;= 1; //x2 us, = 2 cycles

    // account for the time taken in the preceeding commands.
    // we just burned 17 (19) cycles above, remove 4, (4*4=16)
    // us is at least 6 so we can substract 4
    us -= 4; // = 2 cycles

#else
    // for the 1 MHz internal clock (default settings for common Atmega microcontrollers)

    // the overhead of the function calls is 14 (16) cycles
    if (us &lt;= 16) return; //= 3 cycles, (4 when true)
    if (us &lt;= 25) return; //= 3 cycles, (4 when true), (must be at least 25 if we want to substract 22)

    // compensate for the time taken by the preceeding and next commands (about 22 cycles)
    us -= 22; // = 2 cycles
    // the following loop takes 4 microseconds (4 cycles)
    // per iteration, so execute it us/4 times
    // us is at least 4, divided by 4 gives us 1 (no zero delay bug)
    us &gt;&gt;= 2; // us div 4, = 4 cycles
#endif
    // busy wait
    __asm__ __volatile__ (
        "1: sbiw %0,1" "\n\t" // 2 cycles
        "brne 1b" : "=w" (us) : "0" (us) // 2 cycles
    );
    // return = 4 cycles
}

void init() {
    // this needs to be called before setup() or some functions won't
    // work there
    sei();

    // on the ATmega168, timer 0 is also used for fast hardware pwm
    // (using phase-correct PWM would mean that timer 0 overflowed half as often
    // resulting in different millis() behavior on the ATmega8 and ATmega168)
#if defined(TCCR0A) &amp;&amp; defined(WGM01)
    sbi(TCCR0A, WGM01);
    sbi(TCCR0A, WGM00);
#endif

    // set timer 0 prescale factor to 64
#if defined(__AVR_ATmega128__)
    // CPU specific: different values for the ATmega128
    sbi(TCCR0, CS02);
#elif defined(TCCR0) &amp;&amp; defined(CS01) &amp;&amp; defined(CS00)
    // this combination is for the standard atmega8
    sbi(TCCR0, CS01);
    sbi(TCCR0, CS00);
#elif defined(TCCR0B) &amp;&amp; defined(CS01) &amp;&amp; defined(CS00)
    // this combination is for the standard 168/328/1280/2560
    sbi(TCCR0B, CS01);
    sbi(TCCR0B, CS00);
#elif defined(TCCR0A) &amp;&amp; defined(CS01) &amp;&amp; defined(CS00)
    // this combination is for the __AVR_ATmega645__ series
    sbi(TCCR0A, CS01);
    sbi(TCCR0A, CS00);
#else
    #error Timer 0 prescale factor 64 not set correctly
#endif

    // enable timer 0 overflow interrupt
#if defined(TIMSK) &amp;&amp; defined(TOIE0)
    sbi(TIMSK, TOIE0);
#elif defined(TIMSK0) &amp;&amp; defined(TOIE0)
    sbi(TIMSK0, TOIE0);
#else
    #error  Timer 0 overflow interrupt not set correctly
#endif

    // timers 1 and 2 are used for phase-correct hardware pwm
    // this is better for motors as it ensures an even waveform
    // note, however, that fast pwm mode can achieve a frequency of up
    // 8 MHz (with a 16 MHz clock) at 50% duty cycle

/******************** Modified Code for Timer 1 *********************************/
#if defined(TCCR1B) &amp;&amp; defined(CS11) &amp;&amp; defined(WGM10)
    // set timer 1 prescale factor to 64
    sbi(TCCR1B, CS11);      
    sbi(TCCR1B, CS10);

    // put timer 1 in 8-bit fast pwm mode
    sbi(TCCR1B, WGM12);
    sbi(TCCR1A, WGM10);     

    // enable timer 1 overflow interrupt
    sbi(TIMSK1, TOIE1);
#endif
/********************* End Timer 1 **********************************************/

    // set timer 2 prescale factor to 64
#if defined(TCCR2) &amp;&amp; defined(CS22)
    sbi(TCCR2, CS22);
#elif defined(TCCR2B) &amp;&amp; defined(CS22)
    sbi(TCCR2B, CS22);
//#else
    // Timer 2 not finished (may not be present on this CPU)
#endif

    // configure timer 2 for phase correct pwm (8-bit)
#if defined(TCCR2) &amp;&amp; defined(WGM20)
    sbi(TCCR2, WGM20);
#elif defined(TCCR2A) &amp;&amp; defined(WGM20)
    sbi(TCCR2A, WGM20);
//#else
    // Timer 2 not finished (may not be present on this CPU)
#endif

/************** Modified Code for Timer 3 ***************************************/
#if defined(TCCR3B) &amp;&amp; defined(CS31) &amp;&amp; defined(WGM30)
    // set timer 3 prescale factor to 64
    sbi(TCCR3B, CS31);      
    sbi(TCCR3B, CS30);

    // put timer 3 in 8-bit fast pwm mode
    sbi(TCCR3B, WGM32);
    sbi(TCCR3A, WGM30);     

    // enable timer 3 overflow interrupt
    sbi(TIMSK3, TOIE3);
#endif
/************** End Timer 3 *****************************************************/

#if defined(TCCR4A) &amp;&amp; defined(TCCR4B) &amp;&amp; defined(TCCR4D) /* beginning of timer4 block for 32U4 and similar */
    sbi(TCCR4B, CS42);      // set timer4 prescale factor to 64
    sbi(TCCR4B, CS41);
    sbi(TCCR4B, CS40);
    sbi(TCCR4D, WGM40);     // put timer 4 in phase- and frequency-correct PWM mode 
    sbi(TCCR4A, PWM4A);     // enable PWM mode for comparator OCR4A
    sbi(TCCR4C, PWM4D);     // enable PWM mode for comparator OCR4D
#else /* beginning of timer4 block for ATMEGA1280 and ATMEGA2560 */
#if defined(TCCR4B) &amp;&amp; defined(CS41) &amp;&amp; defined(WGM40)
    sbi(TCCR4B, CS41);      // set timer 4 prescale factor to 64
    sbi(TCCR4B, CS40);
    sbi(TCCR4A, WGM40);     // put timer 4 in 8-bit phase correct pwm mode
#endif
#endif /* end timer4 block for ATMEGA1280/2560 and similar */   

#if defined(TCCR5B) &amp;&amp; defined(CS51) &amp;&amp; defined(WGM50)
    sbi(TCCR5B, CS51);      // set timer 5 prescale factor to 64
    sbi(TCCR5B, CS50);
    sbi(TCCR5A, WGM50);     // put timer 5 in 8-bit phase correct pwm mode
#endif

#if defined(ADCSRA)
    // set a2d prescaler so we are inside the desired 50-200 KHz range.
    #if F_CPU &gt;= 16000000 // 16 MHz / 128 = 125 KHz
        sbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #elif F_CPU &gt;= 8000000 // 8 MHz / 64 = 125 KHz
        sbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        cbi(ADCSRA, ADPS0);
    #elif F_CPU &gt;= 4000000 // 4 MHz / 32 = 125 KHz
        sbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #elif F_CPU &gt;= 2000000 // 2 MHz / 16 = 125 KHz
        sbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        cbi(ADCSRA, ADPS0);
    #elif F_CPU &gt;= 1000000 // 1 MHz / 8 = 125 KHz
        cbi(ADCSRA, ADPS2);
        sbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #else // 128 kHz / 2 = 64 KHz -&gt; This is the closest you can get, the prescaler is 2
        cbi(ADCSRA, ADPS2);
        cbi(ADCSRA, ADPS1);
        sbi(ADCSRA, ADPS0);
    #endif
    // enable a2d conversions
    sbi(ADCSRA, ADEN);
#endif

    // the bootloader connects pins 0 and 1 to the USART; disconnect them
    // here so they can be used as normal digital i/o; they will be
    // reconnected in Serial.begin()
#if defined(UCSRB)
    UCSRB = 0;
#elif defined(UCSR0B)
    UCSR0B = 0;
#endif
}
</code></pre>
 32879: <p>Just for the record, I posted this question before I made an account by mistake, so that is why I cannot select best answer; BUT, I found the solution for anyone wondering.</p>

<p>I had the interrupt enabled for more than one timer (forgot to disable interrupts on the timer0 code). Once, i did that the code worked! I was able to move the millis, micros, delay, and delayMicros functions to the 16-bit timer 1!</p>
