I was at the 100 mile mark on the engine so I went ahead and did a head re torque, checked cam chain, and reset valve lash. I also adjusted floats back where they were supposed to be (both set high), adjusted mix screw back to 3/4 turns, and sync'd. I was still experiencing the intermittent stall, so I played with the timing a bit. First I retarded it and it seemed to make it worse, so I advanced it and it seemed to like that.
I took it out for a spin around town and it didn't stall. It did have a little hiccup and one of the stoplights, but the engine didn't die.
Something I had neglected when installing my pamco came to mind. I remembered the part that replaces the advance unit was a little weird. The key ways weren't cut right and I had to "mill" them taller with a dremel so that pins would fit. Also, the key way for the pin on the cam looked to be offset and didn't line up with the axis of the advance rod. To me, this seems like it is retarding the ignition. To get the timing in the normal range I have to adjust the plate to nearly full advance. Is this normal?
I took the bike out again a couple hours later and went for a longer ride on some back country roads, it rode great! Maybe it was just me, but it seemed happier coming back through town at all the stops, no stumbling at stops, etc. I also had the headlight on and it didn't have any effect on how it ran.
One last thing. When I sync the carbs using my home-built manometer the left side always seems to pull harder, although very slowly. I backed the idle screw nearly all the way out and it didn't really do anything.. its like I have to turn them a lot to see any noticeable difference.