Running rough, throwing codes

[Elite1]

My water pump went out last week, sprayed quite a bit of coolant all over the engine compartment.
Took it to a Cummins dealership. They did the following work:
replaced water pump, pulley idler, serpentine belt. While it was in, I had them adjust the valves.
The truck is an 03', HO 305/555, 6 speed, with 109 k miles. They steam cleaned the engine to clean up the coolant mess...
While I was driving home from the shop, got about 5 miles down the road and the truck started bucking and surging. The shop was closed for the night, so I nursed it home, another 5 miles or so.
The next morning I called the shop and told them of the problems, they said to bring it back in...
Instead I decided to try drying out all of the electronic connections with a blow dryer. I was assuming between the coolant flying around and the steam cleaning, water may be the problem.
I dried out as many as I could and started the truck, it seemed to be back to normal. drove about 20 miles and it seemed fine.
Now a day later it has started bucking and surging again. Sometimes the fuel surges all the way to redline, then I push in clutch and it comes back down. Tried drying all connnections out again and even spraying contact cleaner. It didn't help.
Here are the codes it has thrown:
P0111, P0201, P0107, P0642, P0483, P2146. I have already looked up all the codes...
Does anyone have any suggestions ?