The bleeding issue is easy to fix. Spray dark colors first, and let them dry thoroughly before doing the next color. As Mel mentioned with light colors, even if you let them dry the color can change depending on the next color. I back almost every light color with either white or silver before doing the next color. But ya gotta let them dry thoroughly no matter what.
For the body post holes, I always trim and fit my bodies why they are still clear, it is much easier to line everything up, plus you don't run the risk of damaging the fresh paintjob trimming it out after you paint it.