It sounds like it's had a GMC regulator installed at some time, which was positive ground. Your cutout relay probably stuck, which allows the battery to discharge through the armature, shorting it out. Install a new, negative ground regulator, and be sure to polarize the generator before running it, by touching the armature lead to the batery terminal for a second or so to be sure it's polarized to the correct battery polarity. If it's the original 6V system, "closing voltage" on the cutout relay should be 6.5 volts or more, to assure the cutout relay disconnects the generator from the battery when the engine stops, or armature voltage drops below battery voltage. Dirty, or sticky cutout relay points will allow the connection to stay closed, and the generator generally gets fried in the process.
Jerry