How about changing your fuel filter? That probably needs to be done. What brand plugs did you use? These Fords sometimes don't do well on non-motorcraft replacement parts...did you over oil the filter after you cleaned it?
2007 Ford F150 XLT Texas Edition Scab w/ 4.6 V8, Superchips Cortex, AFE Stage 2 CAI, and Cherry Bomb muffler...