sgkoether

Having a serious issue with my truck its a 1999 dodge ram cummins. So, about two weeks ago I drove it home and parked it in my driveway with the window down. Didn't realize we were going to get 5 or 6 inches of rain that night. So it rained in the drivers side soaking everything. I realized it the next morning and put all the windows down to dry it out. Came back later to use it and it started for about 3 seconds then died. Repeated this about 3 or 4 times then wouldn't start at all. I immediately assumed that my raptor lift pump had crapped out because it had been growling a little. Cracked the line on the top of the filter and bumped the starter and it ran fine and seemed to have adequate flow. Next I cracked the injector lines but couldn't get any serious fuel. I figured the injector pump was out, I even though I had replaced it once about 2010. Grabbed my tuner and looked for codes because last time it threw the injector pump code, but didn't have any codes related to the motor. Called a local diesel place to order an injector pump anyway, and told him the story and he said check for the alarm system to be activated putting the truck in lock down. I read up on that and that sounded right. I did all kinds of tricks, locking and unlocking doors with the key, then manually, then tried the auto locks which weren't working. I finally unhooked the batteries and walked away for 4 hours, came back, messed with the locks and hooked up the batteries and it fired right up. Away I went, drove it every day for a week. The only problem I had was the drivers window switch wouldn't control the window except here and there and the power locks weren't working. Once I tried to roll up the window and the dome light came on. I figured the switches were shot from getting wet.
Parked it in the shed and came out the next day to take off and went back to same problem. 3 or 4 starts for 3 or 4 seconds then no start at all. Did all the same battery disconnect and door lock things. Nothing, Replaced the drivers side window and lock switches, Nothing, Jumpered across the door lock sensor for the key, Nothing, Went to a friend and borrowed a SnapOn Solus scanner and hooked it up. No codes for the injector pump. Only one code for the motor that said reduced power because of overheat. There were other codes in the transmission and ABS but nothing that should deal with it starting. When I went to "Body" the scan tool could not communicate with the truck computer. I couldn't see codes, I couldn't run tests. I thought this was all controled by the CTM so I ordered a used one online and plugged it in and Nothing. Now I am sure I could have gotten a CTM that was already bad but what are the odds. I hooked up the scan tool again and nothing changed, I still cannot communicate with the computer for the "body" side of the truck.
It is my understanding that when the VTSS is activated it will stop the truck from starting. When things are working as they should it sends a signal to the CTM. The CTM in turn sends a "ok to start" signal to the ECU and the injector pump pushes fuel through. Am I mistaken? I am out of ideas. As a side note, the power locks, dome light, chime, etc don't work. I don't care if they work or not but I think it is connected to the starting issue. Any help would be greatly appreciated because this is my only farm truck and I can't get crap done without it.