Yes, I believe the glow plug relay was the cause of the short. I had found that with the truck off and the ignition key not turned at all, the glow plugs were still getting 12 volts.... seems like the relay was stuck "on". The symptom of the batteries draining to 5 volts within an hour or two and the spark when connecting/disconnecting the battery leads both went away after replacing the glow plug relay. Also the wires were not getting 12 volts when they shouldn't have been.
The other repairs were just good things to do once I was in the business of re-wiring things.
May all repairs be so thoroughly successful for all of us.
GentleGiant