Crap I didn't see your question pop up back in April, sorry for the delay. Yeah it's easy to drop parts down there when you're taking things apart. As long as the timing marks line up it doesn't matter where the master link of the chain is when you assemble it.
You can use spray paint that you would find down at any hardware store. The engine never gets hot enough to boil regular engine paint off at all. You can get glossy engine paint and everything. If you want it to shine use another coat of clear. If you go to a auto parts store you will see all kinds of paint for this. Powdercoating is a waste on these engines and you''ll have to completely strip it down which will take you days. And I haven't really seen powdercoating hold up to engine heat too well. Maybe the flat or krinkle coat DuPont but if you use a glossy or especially a clear you will get discoloration form the heat over time. From my experience anyways. If anyone knows of a special brand that doesn't fade or discolor under this kind of engine hear or abuse I would like to know.
Also here is my thread about painting my engine:
http://www.fourwheelforum.com/showthread.php?t=102