I know this is a shot in the dark, but your problem sounds like the same I experienced in Kansas, in January of 2006. We stopped in Hays, because I wanted to get the local Dodge dealership to spray a Toff Liner in the bed and put in a B&W turnover gooseneck hitch. It was extremely cold, when we left the motel, and I couldn't get the truck to start. It took a good several minutes for it fire up and, when it did, the truck ran like crap... . coughing, wheezing.
We got to the dealership, and I described the problem to them. They told me that it sounded like they needed to replace the injectors, but they needed authorization from Star Center which, after three days of waiting, I said screw it and kept going on my trip... ... . this is where your situation sounds like mine..... while it was in the shop, where it was warm, the truck fired right up. The dealership told me that they couldn't understand it.
Long story short, when I got back to Maryland, I took it to my dealership, and they told me that there was a little-known TSB out to reprogram the truck for the injectors... fixed my problem, and I never again experienced those symptoms again.
I wish I could remember the TSB #, but this was three years ago.
I hope this helps a bit.