Finally got my bike up and running again (put in a different, known running, motor) but the clutch seems to be acting up.
Clutch engages/disengages normally and shifts easily between 1/N/2 when not running. Once it is running it seems to want to grind into first (not all the time) sometimes doesn't want to go into 2nd unless rolling and neutral is very tough to hit. I have adjusted the clutch arm and both cable ends per the Honda service manual.