I have made a couple and it isn't that difficult...but in saying that it does depend on exactly what you want to build.
Acoustic guitars - really hard work, as every decision will have impact on tone
, so I'll just talk about electrics:-)
We have discussed winding your ownpickups - doable, but probably not agood use of your time.
Necks - can be very challenging.
Thisis one area I haven't mastered, soended up buying ESP necks (which Ilike as they make some very fast,reasonably slim necks)
The body is a piece of cake - as longas you have decent woodworking toolsand experience.
A table router makeseverything really easy.
Choose yourwood sensibly (for my first one Ichose a really hard Malayan pine, andwent through router bits incrediblyfast - but that guitar has lasted me23 years so far, so it is prettystrong)
Electrics make a big difference.
There are plenty of example circuits, all of which sound different, so if you are a beginner I would go with one similar to the classic Stratocaster circuitry.
Passive and very simple.
I would recommend two books above all others.
The Melvyn Hiscock "Make your own Electric Guitar" and Ralph Denyer's "The Guitar Handbook" as they are very well laid out and explain the trickier bits well.
Best of luck with it - it takes a long time to do well, but it is so rewarding to use your own guitar up on stage.
Out of all my guitars, the one which feels fastest is still my original home built one.
music.stackexchange.com/users/104/Doktor Mayhem
I would strongly advice getting a book for this, as there are many steps and you will want a complete thorough step by step guide.
I would suggest reading through the book before starting the project.
This way you wont get any nasty surprises in the middle of building.
I don't think you will find a good enough source online (at least for free) to make a really good guitar.
By reading the book you minimize the risk of doing the same mistakes that other first time builders do.
Here are a couple from Amazon:
Build your own electric guitar
Make your own electric guitar You will need a lot of patience and a lot of time.
The hardest part to build is the neck, so you might want to think about buying a neck and only build the body.
However, if you have time and some skill there is no reason not to build the neck as well.
I would have low expectations for the quality of your first own built guitar.
It won't be a PRS...
But you will learn a lot while building and your second one will already be a lot better.
However if you do things right you will get a very nice and at least personal guitar!
I have built one myself
and I never use it, since I like my Tele better...
But I am totally going to build another one sometime when I have time and a place to do so.
One more advice: When deciding on the shape of the body I would recommend building a shape that does not exist (unless you really want it to be a Strat or Les Paul) since this will make your instrument a lot different and much more personal than by just making a copy of something else.
Good Luck!
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Just to add to @mrbuxley's great answer: Unless you have access to some serious equipment this is going to be a very expensive and time consuming venture
;).
You might be better off purchasing a pre-made neck and body from a reputable manufacturer such as Warmoth and then assembling all the parts yourself.
The fun part about this (well for me anyway) is picking out the finish, all the hardware, building the electronics with my own crazy circuits, and knowing that I have an instrument specifically designed and suited to my every whim.
Also, if you go this route you could have the instrument in playing condition less than a couple of weeks.
If you build your own from scratch--including purchasing blanks to mill the body and neck from, you are going to have a lot of scratch in the guitar.
Also, finishing a guitar is a black art.
I have friends who have tried and gotten varying degrees of success--but as @mrbuxley indicates your first attempt will never be as high quality as what a professional painter can do; and likely your second, third fourth, fifth, and well you get the idea.
You could spend a couple of years perfecting your technique in this single area in order to get to luthier grade quality.
So, my recommendation is to head over to Warmoth's site, find a body you are in love with, pick a neck that compliments it, go buy all your hardware, and be up and running with your new guitar in a couple of weeks.
However, if you truely are hardcore, and wish to build watch your instrument go from a solid block of wood to something beautiful then prepare for a serious learning experience and a very time consuming but rewarding process.
And who knows, if you get really good at it, you could be the next John Suhr selling your guitars to the likes of John Mayer, Mark Knopfler, and David Gilmour.
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There's been a lot of advice to buy a ready made neck, and if your woodworking skills aren't top notch that is a very good plan to begin with, but if you want to get a little more adventurous you can buy pre-slotted fretboards from some places like
stewmac which takes a big part of the pain out of the equation, especially if you want to do something different to a traditional bolt-in neck, like a neck through construction or something.
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I'm not sure how "from scratch" you want to be.
If you find yourself in over your head starting from say, a large tree and a mound of iron ore, you might want to look at some kits or components .
music.stackexchange.com/users/94/gomad
I want to make an electric guitar by myself from scratch. How can I do this?
Building an electric guitar from scratch
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The  Melvyn Hiscock "Make your own Electric Guitar"  and  Ralph Denyer's "The Guitar Handbook"  are excellent books if you want to build your own electric guitar as they are very well laid out and explain the trickier bits well.  The hardest part to build is the neck, so you might want to think about buying a neck and only build the body. You might be better off purchasing a pre-made neck and body from a reputable manufacturer such as Warmoth and then assembling all the parts yourself. The  Melvyn Hiscock "Make your own Electric Guitar"  and  Ralph Denyer's "The Guitar Handbook"  as they are very well laid out and explain the trickier bits well.  By reading the book you minimize the risk of doing the same mistakes that other first time builders do. The hardest part to build is the neck, so you might want to think about buying a neck and only build the body. However, if you have time and some skill there is no reason not to build the neck as well.  You might be better off purchasing a pre-made neck and body from a reputable manufacturer such as Warmoth and then assembling all the parts yourself.
The  Melvyn Hiscock "Make your own Electric Guitar"  and  Ralph Denyer's "The Guitar Handbook"  as they are very well laid out and explain the trickier bits well.  By reading the book you minimize the risk of doing the same mistakes that other first time builders do.  The hardest part to build is the neck, so you might want to think about buying a neck and only build the body. However, if you have time and some skill there is no reason not to build the neck as well.  You might be better off purchasing a pre-made neck and body from a reputable manufacturer such as Warmoth and then assembling all the parts yourself.