Whether you paint or powder coat, to do the job right you have to take off the cable guides (as well as the downtube shifter mounts, but that's a whole 'nuther story). I've refurbed a lot of these older Cannondales and have yet to find a way to remove the guides and re-use them. They use a funky tube-within-a-tube system (and them tubes are teeny) that's semi-molded into a new guide. So I just buy them from my Cannondale dealer for about $8 for a bag of three. One bag for each bike. Cost of admission, I guess.
But I have a bunch of guides in good shape and someday I'm gonna figure out how to securely remount them buggers.