Over Advanced Timing
Colt - just throwing this out there, but did you buy the truck used? If so, are you sure it doesn't have a custom tune on there? Some dealers will keep or toss a tuner on a trade-in without bothering to check if it's still tuned.
thump might be on to something, as an example, i bought an '03 focus svt a couple years back, it was misfiring badly when i bought it, replaced the plugs and wires and that helped, but it would intermittently run bad and the check engine light would come on. i figured out the guy who had it before me had some SCT tune on there, I took it to Ford, had them program it back to stock, haven't had a problem since, i would try that route
Yea I did buy it used and I never really thought about that but when I had the phasers and all that stuff replaced the dealership reflashed the PCM so wouldn't that clear that out? Oh and they also took the PCM off another truck to run it on mine and it still ran rough.

