I painted mine separately, too. When I realized the gap would be visible, it just drove me crazy and I decided to fix it. But I seem to remember it cost me at least a month of headbanging, first.
On the other hand, it would probably be difficult to paint them well if installed first.
Don't worry about inserting the engine. It's tricky, but certainly not difficult- even after the firewall and exhaust components are installed. I must have test fit mine dozens of times. I think it may be installing the plenum/air cleaner assembly that makes it difficult or impossible to remove, and that can be left until very late in the build.