I'm using a copper head gasket, so I kinda wanted to be able to see it sticking out, so I painted before assembly.
That's funny about the seal, I originally installed the rope, because I thought I read that you couldn't use the neoprene in motors older than 1959. Then I read your post about it, and re-looked at the packaging. Out went the rope! Luckily, I was able to make the switch right before I installed the oil pan. Which is a PITA. FYI, I put the cork down on the block first, then the rubber end gaskets, then the pan on. I've read to put the gasket on the pan, but I don't know how you would do that unless you try to stick the end gaskets to the pan too...