I've gone through the strip and repaint process a couple times with factory and PO paint. The best option I've found is to remove the engine from the frame, leave everything intact (but remove the carbs and exhaust), and then lather it with paint stripper. Look for the paint stripper specifically formulated for aluminum so you don't get the white corrosion build-up after you remove the paint. Then, hose the whole thing down with a garden hose, dry it, and scrub with one of the red paint prep pads (available at most auto stores or Ace Hardwares) and degrease the surfaces. After that, you are ready to paint.
When applying the stripper, and subsequently hosing down with water, make sure to plug the intake and exhaust ports. I just use a few bunched up paper towels when I do it, and am careful with where I direct the water spray. You don't need to worry too much about a little water getting in there, but make sure you don't douse the intake or exhaust ports with direct water flow.
I use the engine enamel I find at Kragen (dupli-color), and have found that it holds up well even for screw heads. I prefer to remove as many screw/bolts as possible though, and mask off small circles where the screws/bolts will contact. If you don't do this, then the screws/bolts will tear the new paint away when you screw them in. If you leave the screw/bolts in when you paint, then the paint will tear when you first remove them.
Of course, disassembling the entire engine and painting the surfaces individually is always the more complete option.
The only point to bear in mind is that the paint will likely become very soft the first couple times it is heated up. So, make sure to heat up the engine and let it cool a couple times before you ride it to keep road debris from nicking your new engine paint.
Good luck,
Camelman
