CF is pretty rough on drill bits, and they will tend to "walk" when you're starting the hole. There are bits called "centering" bits or "center finding" bits, I don't remember the exact name, that have a very small sharp point that don't tend to wander as easily as regular bits. If you're using a drill press, it'll be easier in any case.
I've not run into any cracking issues, but if you're going to drill all the way through the CF, you'll want to have a piece of hard wood or plastic behind the CF or the drill WILL tend to delaminate the CF as it exits leaving a ragged looking hole.
Motor rebuilding tuning:
http://www.motortuningsecrets.com/
it's about tuning a stock motor, but much of it applies to rebuilding. you can ignore the bushing polishing stuff if it's not a brand new motor.