Hello bancika, and welcome to the forums. Have you checked out the behemoth of a thread over in the electronics section? If not, I suggest you go take a look. It is 125 pages long, but just about all the information you could ever want is there.
I'm not exactly sure why you are under the impression that you would have to do any drilling into your guitar. Assuming your control cavity is large enough, you shouldn't have to do any alterations to your guitar.
If you read the other thread, you will find out that this sustainer system is pretty much reliant on psw's thin driver concept. In fact, it's be speculated that a coil with a thickness of 3mm or less is optimal. I would urge against a surface mount system, though, because you wont be able to adjust the coil. Because it is easier to drive low strings than it is high strings, in order to get (more) even performance, the driver should be closer to the treble strings and further from the bass strings.
What do you mean too far when you mentioned mounting the driver next to the neck pickup? If you mean between the neck pickup and the neck, that wouldn't be a problem at all. In fact, the closer the driver is to the middle strings, the better it works.
Do keep in mind that if you plan on keeping your neck pickup (or neck and middle in the case of a strat), you will have to have some sophisticated switching to completely remove the neck pickup from the guitar's circuit. If you don't, you will have MASSIVE EMI feedback.