Gone through 3 whats? Batteries or alternators? Have you fixed the physical problem yet?
The short of the +12 V to the starter, large one, to ground could have fried some sensor ground wires, like the O2 sensor. I would charge the battery to a full charge, and then pull all the connections at the starter relay, near the battery,
http://www.naxja.org/forum/showthread.php?t=1073495&page=2
then connect one wire at a time to the large post (connect the + battery wire first to that post) and look for a voltage drop at the battery. Or just jump one hot wire at a time to the battery + with a 10 Gauge (apx) jumper wire (might add a 30 amp slow blow fuse to the jumper wire).
That would test the + wires one at a time. The ground wires are mostly at the oil dip stick and they can always be a problem just making good continuity to the battery ground on Renix jeeps. You could also disconnect the battery and test each + wire for continuity to ground using Ohms scale and if you find one that is say 10 ohms or less, it is likely shorted ground.
Could be missing a ground at the alternator, but I doubt that from I read so far. In fact it does not sound like a ground problem yet (might be later once you fix the power drain issue!!!)