The failure to run right sounds like electronics based on other electric issues. I quickly changed a lot of wiring, power, alternator stuff on my car, so I don't recall how the exact stock system works, but it sounds like your voltage regulator is bad. It could cause a good battery to drain, kill a fuel pump or pop the fuse, maybe smoke a ignition setup, etc. Definitely the kind of intermittent (maybe heat based) issue electrical stuff could cause.