I was having an issues with a dead battery, I figured it was because I was using a 1.2 ah 12 volt battery which worked pretty well actually as long as you could get the bike started pretty quick, which most of the time wasn't an issue. Alas those times I forgot to turn the ignition on or choke it and the battery would die while I was kicking like crazy was getting annoying.
So I crammed a 7ah battery under the seat, problem solved for a few rides anyway then it was dead again. First thing I thought of was the charging system particularly the regulator, as it was the only old original part beside the stator and field coil and they checked good. My charging voltage, however was only 12.2 volts. Then I find out you can adjust the output on the regulator, awesome!
Cleaned the points in the regulator, hook up a charged battery and adjust the thing. It's now putting out 14.5 - 15 volts at or above 5k rpm, just like the manual says. There is a whole procedure outlined in the manual if anyone else is having issues with low voltage. A quick Google search should point you in the right direction, if you are interested.