Sigh... sad demise to an otherwise pretty decent 80's cruiser.
More often than not if it isn't caught in time the reverse hookup will do all of what mlinder said and more.
Yamaha was using some nasty bad electronics then (almost rivaling suzuki in the 70's) and even the slightest spike in current would cook em.
Another thing to check besides the coils would be the fuse terminals. Make sure none are melted or deformed in the housings. If so, they will give you loads of trouble later in life.
My 80 XS850 just got a 80% rewire because of poor battery vent design.
Hope you figure it out.