Great points there OldWizKid. I can only add some minor tips after that!
I'd really recommend to not move the painted parts. I'd get the parts in the area and do both paint and dry in the same spot. Having the paint, part, and air at the same temp is a big deal IMO. The largest flaw from having several different temps is the dreaded Orange Peel. The bottom dries faster or slower than the top layer. A variation of orange peel also occurs from over application.
And if anything else, you risk screwing up by moving the wet parts around. I agree with the sun being our curing oven, but only after the paint is set, which is about 45minutes. Once it's set, I think it's fine to move it around, peel the masking, start to cure it, and do whatever.
I peel my masking off early on some shoots. If you pull it off after it's set, you can have rough edges. That's fine if you color block (sand) before a clearcoat or something like that. But if you don't plan on that, peeling the mask early has it reform a smoother edge by the paint slumping or relaxing. It's a bigger deal if you're making a design or mating two colors. Not a big deal if you're just coating a big area and no edges exist.
I love the idea to gut the cases as much as possible. It's just easier to work with, and you can get details you usually can't in an assembled case.
Nooks and crannies are covered. If you paint assembled, these gaps can be covered and later crack. Or worse, it's a removable part you later want to remove.
I'd tape off some areas that could become problematic in time. All those little standoff holes should be left bare. If you can find some little round stickers, they work perfectly for masking these spots. If not, just tape 'em up. When the board's on, you won't see them. Might just mask off the entire square area where the board goes. No need to waste paint when you won't see it.
I'd also go ahead and mask off the rear PCI slot's top. Fit up a pci blank or device to see where you need to mask.
I don't paint this area because it's not electronically sound, but really isn't an issue overall. Mainly, it's because you change parts and it'll get scratched up or worse...begin to chip. I'd also skip doing the inside where the PSU mounts for the same reasons.