Buck, bike is coming along great!  Don't worry about all the failures popping up, they are just growing pains.  a 25 y/o bike will have them anytime you start adding power to old parts.  Just a good thing they are all happening now instead when you're out riding.   More will happen, that's for sure.  But once you get all the weak areas addressed, a built zilla becomes very reliable.   Knock on wood, it's been about 4 to 6 seasons since i've had anything break.  Worst thing that's happened is a bolt or 2 falling off. 

One last thing, have you had the flywheel hub welded?  if not, DO IT!  It will fail!  And likely take out your stator and stator cover with it.  Once you add any power to these bikes, the flywheel is one of the first things to go.