Got my truck back yesterday and all is well so far!!
After replacing several parts, the final major component malfunction turned out to be the FCW (according to the dealer). They said an electrical fault was causing the FCW to believe a crash was eminent. This was causing it to override the trans shifting ability.
Also, after replacing the trans control module the 4x4 did not work. They said they had it on the lift and only the rear wheels turned! (That would have been fun for me at first, but winter is coming!!) After that call, I never got an explanation on what caused it or how they fixed it.
I asked for a print out of the work that was preformed but they hesitated and said they would mail it to me within a week. They handed me my key, and off I went with not even a page!. All they said was at least a thousand dollars in parts were replaced. I don't feel everything was kosher with that.
Why would the FCW need the ability to control the trans. I understand it would control braking and acceleration during cruise, but the trans? Questionable to me (not that I know anything about cars).
I will update when I have a more logical picture of what went wrong. Hopefully the print out will be given to me in its entirety and that should give us a better explanation.