2007 Columbia current draw

I have a 2007 Columbia with a 12.7 dd with an Eaton Smart-Shift automatic. I bought the truck last year, it sat for a month before I started using it. Everything worked fine.
I returned from a 2 week trip and went on vacation. When I returned the batteries were dead. I charged them and everything seemed to work fine. On my next load I noticed a slight miss so I took it to detroit diesel shop in Reno. They changed a fuel injector and wiring harness and when I went to pick it up the batteries were dead. When they jump started it there was an arc when he hooked up the cables.
On the way home the ac did not blow cold, I checked the freon and it was ok. the next day I went to take it back to detroit and the batteries were dead. I jump started it and took it back to detroit. The technician had broken the power wire to the compressor when he was working on the injector.
I brought it home again, everything seemed to work fine, but the batteries go dead in 4 hours. With fuses and everything in power at the AC compressor is always live. When I unplug it and pull the negative off of the batteries there is a 12v draw. I have pulled all fuses and relays out and there is still a 4v draw. There are 3 fused leads off of the batteries themselves, and with the key off 2 have 3.5v draws and the third has a 12v draw.
Also, with the key off if I switch the paddle shifter I can hear clicking in the transmission. I have unhooked the power wire from the alternator and the current draw is still there.
Have any of you experienced this? Do you know of a fix?
Thanks!