They probably have the battery hooked up backwards... it goes from front to back:
Radiator Core Support to front battery Negative
Front battery Positive to rear battery NEGATIVE
Rear battery Positive to firewall positive buss bar (upper one).
I'd put money on the fact that they probably hooked up the cables like a 12V truck and that just don't work well... it lets LOTS of magic smoke out along with a lovely fireworks show under the hood. Make sure you check out the charging system when you get it back together, they might have fried the diodes in the voltage regulators. Make sure you get the correct alternators, they are special Isolated Ground alternators, NOT standard case grounded ones.
Later,
Joe
Edit:
You are looking for TM 9-2320-289-20
This is the intermediate maintenance manual. You should also download the other manuals that start with the same set of numbers but end with -20P, -34, and -34P. The -P manuals are the parts manuals that contain the GM part numbers for nearly every part on the truck. You can also download the -10 manual which is the operator's manual.