Quick question for everyone, and I'm aware this is mostly your own personal taste, but the bass drum hoops are missing a bit of paint in a few places. Do I paint them, or just leave them as is? Or do I go a bit less conventional (I assume) and sharpie them?
You're correct, it's up to you based on your personal taste. I know many purists wouldn't touch the hoops, but others would. Personally speaking, I think it depends on the drum. If it's truly a timepiece from the early 1900s or something, and restoring it might reduce the value, I might not touch it. But if I had your kit, I'd probably paint the hoops eventually.
Case in point: I've owned a 1969 Rogers for about 17 or 18 years that's in really good shape other than some dust and dirt. Lately I've considered disassembling it to clean it up, and if I do that I will likely paint the hoops. It would really make the kit look new.
Finally, when taking the lugs off, should I worry at all about making sure each lug finds its original spot again, with the same screws, or is a lug a lug, and a screw a screw?
All the holes should be precisely drilled to accommodate any of the lugs. This was true even on my cheap MIJ kit.