I would try to find out what is wrong with the car by setting it back to stock - tune, plugs, intake or whatever. It may be anything that throws off your AFR / vacuum leak, poor fuel quality (I only try to use Shell 93), or bad spark (coil). Run a diagnostic log to see if there are any error codes pending.
That is great advice and I fully agree, but I have gone rogue because I had my truck at the dealership more time than I had it at my house during the first six months of ownership seeking their assistance trying to fix this issue and a gas pedal vibration issue. The gas pedal vibration was finally fixed by me after endlessly testing numerous other "solutions". What ultimately worked for me with respect the gas pedal was replacing the resonator with an X-pipe that removed what my dealer called a "harmonic frequency" vibration. The X-pipe seems to balance the the pulses in the exhaust pipes and thereby gets rid of the frequency that caused the gas pedal to vibrate like a cell phone on vibrate mode.
Regarding the "stutter" under acceleration, they seem to be unable to help unless the truck is throwing codes, so I am trying everything, similar to the gas pedal situation, to fix it on my own, hence, several different types plugs, running only Shell gas with 93 octane, purchasing a tune, etc....