Also I would look at the MAF sensor as well. An incorrect mixture of air/fuel can cause a weird stutter too. Simply take the sensor out right after the air filter and use some MAF sensor specific cleaning solution and jet it off.
Idk if the dealership did this or not when you had it there, but you could have them reflash the computer back to a stock tune in case there is an updated tune for the computer. However if you are running a new tune from an aftermarket tuner, just use that tuner to reflash your computer.
Hope you can get your truck straightened up man!
-2011 F-150 Lariat: 5.0 "Coyote" V8, 6-spd Auto (6R80E), 3.73 ELocker. White Platinum Metallic Tri-coat.
-1992 Ford Ranger: 4.0L OHV, 5spd (M5OD-R1), 3.27 Open.