Jeff,
Man, you just have to take a hard look at the frame ground where it comes from the battery and make sure you've got good, clean contact before you toast your regulator or even worse, the ignitor. Then double check the multi-plug from the regulator (it's down near the swingarm mount) that runs up to the fuse block and make sure that's good to go as well. I'd bet one of those two is the culprit.
