I do already have 3 points on my record for alcohol-related convictions, yes.  What will happen if I plead guilty now?
a guilty plea to a violation that results in 5 or more points may result in the revocation of your license according to the Commissioner's Regulations.  You may want to consult with an attorney before entering your plea.
What do I do now that I've ordered a transcription for my appeal in the status of an online appeal?
You have to mail the additional arguments to the Appeals Board before 30 days have passed since the transcript you ordered was sent to you.