Update 19JUN14 1610: Had the meeting a little bit ago and I'll say we made some really good progress and I have a lot of answers now. The service manager started off by giving me a loaner vehicle. He said that the goal is to get the truck done before I leave but in case it is not done, he will provide a vehicle for me until the truck is done and then he will take care of getting it sent to Indiana. They are also going to make sure all of the workmanship issues are corrected and that any issue they can resolve will be resolved. Insurance agent was informed of what they were getting into as far as a possible replacement of the entire wiring harness. They are going to return the truck back to stock (disconnect all lights and accessories) by Monday and see how the truck behaves then. They want to work with it at a factory level so they can troubleshoot what is going on better.
My concern is that they said I put it in the mud again. They were convinced I had sunk it twice and that they hadn't seen some water intrusion in a wiring harness before I brought it back this time. I'm not sure what would make them think that I put it in a water hole again. Even though it saw a little mud in NC it did not see anything that would have caused new water intrusion into a wiring harness. I assured the service manager that this had not occurred, whether he believed me or not is unknown.
The real kick in the nuts was that after talking things over we walked back to look at the truck so they could show us what they were talking about. The insurance agent looked at me, apologized for the way everything has happened, and then informed me that if he had known how much water had actually came into the truck he would have totaled it. He didn't see much physically because I had thoroughly cleaned the interior before originally taking it to the dealer. What he saw was a clean interior with wet carpets. The way I understood it, now he can't consider it a total loss until the repairs reach 75% of the total value in VA.
I will be stopping by the dealer at 1500 on Monday 23JUN14 to see what the dealer has found and how everyone wants to proceed.