So after you started the bike using jumper cables, the bike kept running? Were you able to charge the battery while it was off the bike?
Did it die just while you were cruising down the road, or did it refuse to start after you had parked it and left it to sit? (From your story, it sounds like you were riding along, come to stop or something, and the bike quit. But if it was able to restart and run after being boosted with cables, then I would suspect something other than the rectifier. If it kept running, even with a shit battery, you know the stator and rectifier are fine, right? (Someone correct me if I'm wrong, cause I hate electrics.) Certainly it didn't keep running even after being jumped....
I'm also surprised that you can control when your headlights are on or off. We are forced to have them turned on in the states, all the time.
Or do you mean that they wouldn't come on?