[Overdriven]

I use a body reamer for body posts and smaller holes. I also have an assortment of bimetal hole saws for larger holes that work well on lexan, just go slow. The step drill bit is a good idea too, I have a couple around. I agree with BrianG about using a sanding drum on a dremel, works great for enlarging holes, smoothing out cuts in the wheelwells etc.

I think drilling holes after the body was painted is a holdover to the days when bodies didn't come with overspray film. Personally I always have my bodies ready to mount before paint, as I've messed up the paint while trimming it out. I just take my time trimming so I don't mess up the overspray film to much on the edges (if I do a little tape and its fixed) and I haven't had any problems.