Hey welcome to EM, fellow necromancer of Insights
The primary batterys are a DC setup so you shouldn't be reading a negative voltage. Where are you taking your readings from? The two posts inside the pack or else where? You might have to gut the pack and manually cycle the batteries to bring them back to life. How has your rebuild being going?
Heres a link to some of the work I have done to mine, most of my repairs so far have been mechanical in nature.
http://ecomodder.com/forum/showthread.php?t=1263