Bike is all back together. Still not running as smooth as it should and the idle hangs a couple grand too high then drops back when it is up to operating temperature. Checked the compression and it's 150,140,140,150 so that was good. Most of the valves were too tight, especially the exhaust so they were all adjusted. It must have some of the cheap points installed, because the dwell was off and when I set it to 46-49 I didn't have enough movement on the timing plate to get the timing aligned. I'm going to try the tricks Hondaman mentions to see if I can reset the dwell and still get the timing set right.
It seems like it might be too lean, so the next step is to take the carbs back off and see if the emulsion tubes are blocked. I didn't think about doing it on the first cleaning and I am regretting it now. Are there any tricks that allow installing the carbs with the air cleaner plenum installed? Getting the plenum back on the number 2 and 3 carb was a royal pain.