So not much to report - I've put a few miles on the bike and been playing with the jetting some more. The main jet I installed at first - 117.5 - seems a bit fat, actually, but the midrange is kinda lean.
I don't want to spend much time with it because I plan to either install K&N "pod" filters or swap a set of VM29 smoothbores onto the motor. Either approach will require some serious jet swapping, so I don't plan to spend a lot of time on this interim setup. I managed to brown the ends of the header pipes while I was tweaking the mixture screws, of course, but most of the color polished out. I've heard it's an inevitable process with aftermarket pipes.
In the meantime, I was annoyed by the top end rattle that I hoped was an exhaust leak. It wasn't. I pulled the valve cover off yet again and measured all of the clearances - I swapped around the shims some more to get them all on the tight side. The clatter seems to have gone away, but I have yet to ride the bike any distance. Hopefully the noise was just a sloppy valve adjustment on my part.
If not, I'm not sure the valve cover gasket will survive another removal, but we'll see, won't we?