Update: The problem seems to be getting worse; runs like crap, truck shakes, etc until it warms up then everything is fine. So I took it to the dealership today for a reflash and the "service advisor" asks me why I want to pay $95 dollars for a reflash that may not fix the truck. At this point he hasn't even asked me the symptoms. So I volunteer the symptoms and ask again for the reflash. He says again well a reflash might Not fix it. I say OK but it might. Then he asked if the CEL is on and I say no. At this point he is gettin kind of smart a$$y so I say just let them reflash it so I can be on my way. He snaps back "ok, but you'll have to leave it a couple days". I say no thanks and left. I thought a reflash could be done in the parking lot in a couple minutes.
Anyway, when I get home I call a small dealership that is usually better to deal with and ask if i can bring the truck in for a reflash and wait. They service advisor says sure, but it might not fix the problem. He says that he will be glad to run diagnostics on the truck and tell me what the problem is.
So I will go there tomorrow and see what the problem is. I've got a feeling its an injector or two. I'm gonna be pissed if I have to pay a couple thousand bucks before I make the first payment.
On a side note I drove it to Daytona Beach, Fl and back over the weekend about 750 miles round trip 85mph there and back. No problems except for running like crap when first started in the AM