hi, i experienced a problem a while ago, like you my headlmp fuse was blowing it turned out to be a bulb failure. it had shorted internally, at least an easy fix.
i think it was gulg, he had a problem under the seat, the loom passes a post/ allen bolt and it had rubbed through the insulation. as per usual the fix is easier than the diagnostic

as for the regulator, i dont believe the short out, other than blowing fuses and draining batteries would cause a failure, as the stator/ generator is not a big capacity unit. my money would be on the connector particularly the earth terminal.

personally i would change it out for a beefier unit, most five wire bike regulators can be made work check out http://www.xt660.com/showthread.php?...ight=regulator

hope all gets sorted bernard