I know its been a while. I have been busy with a lot of other projects, but I didn't want to leave this unfinished. I put a baffle in the exhaust, and it sounds/runs better. I believe the hard starting issue was related to the ignition...
After I cleaned out the tank and carbs again, it started up better and the baffle seemed to help as well. I gave it back to him, but he called me once again. He was riding, and it just died, would not start again. I went over to his house to start one system at a time, Checked fuel delivery and it seemed fine. next I went to check compression and valve clearance. Thats when I found the problem. When I took the points cover off to use the timing marks to check the valves, I noticed the nut on the end of the advance shaft was loose! It had enough play to let the advance unit slip out of the keyway and it stopped spinning. Tightened, cleaned the threads, new nut, and some loctite. Runs amazing now!