I guess I need to complete the thread - it's done. I managed to fire it up, adjust the timing and carbs and put about 100 miles on it. No smoke, good power, no weird noises - it seems good.
A few minor issues - I had a leak from the primary and the clutch wouldn't disengage fully (making finding neutral impossible). When I pulled it down, I found the infamous circlip behind the clutch basket deformed and out of position. Yes, I did only torque to 40ftlbs, but it still failed. When I replaced that, and the seal - the leak went away.
I also found the neutral light switch was screwed in too far which also screwed up finding neutral. This adjustment seems kinda touchy. I think either my switch is going bad or the bump on the shift plate is worn. I managed to find a workable medium.
All in all, I'm very happy with the bike and hope to get many miles out of it.