I've finally gotten around to installing the upgraded regulator and new horn in addition to some maintenance items. I noticed the fuel line had failed, so I replaced it with fresh fuel line. I repositioned the clutch cable correctly only to find that the bolt holding the lever arm at the engine is severely stripped. I also cleaned the air filter, which was in desperate need.
I was unable to reproduce the charging problem I had been noticing. It seems to be charging just fine right now.