Put it back to stock and haul it to a dealer, its still under warranty.
Drive it 50-100 miles to get rid of the p1000 code before taking it in.
BTW
What's your hex code?

08 5.4 Supercrew
 

I experience the same symptoms in my truck and only on #2 tune. It doesn't do it on tune 1 and 3. Since 2 is for towing, I just decided not to use it unless I'm towing, which isn't too often. And when running on #2, and the truck misses, I usually pull over immediately, turn off the truck and it stops the rough running for another two weeks or so.