Well, after the dealer had my truck for a week they are finally done with it and all they did was re flash it... They said the flash was not under the 100k warranty but they did not charge me anything for it. When they called me and said there was no bill I asked them about an oil change - they said $86, it cost me $77 to change it myself, so I told them to go ahead and do it.
They later called me and said the truck needed two new batteries. They wanted $194 each for the batteries. I called a buddy and wound up getting Optima Red Tops for $131 each and put them in this evening. The engine does spin over much faster than it did before, I just hope the reflash fixes the cold start issue. Of course we are past most of our cold weather so I will not know until next year when the warranty is gone...