You should be running Brisk plugs or my fav Autolite HT0 (thats a zero) with a gap of .032. How many miles are on the truck? How long has she been sc'd?
It is possible for the VCT to get gummed up and fail to operate correctly. However I haven't heard of this causing the misfire codes you have. Nothing is impossible though. The 04's have a rep for bad VCT actuators. And these actuators do not like oil thicker then the reccomended 5/20 though some have switched without problems.
someone told me to you were the guy to ask questions about a supercharged ford, i have a 2004 f-150 with a 5.4 it has a cai, cat back system, and a roush tune with a non/ic roushcharger im wondering if i should be running different plugs and gap with that set up. i like the truck and the set up but i have been having coil problems 4 bad in six weeks and i was told they were all new coils and plugs. have u ever heard of the cam sensors under the valve covers getting gummed up and sticky to the point of making the computer say its a coil that is bad on a cylinder thats misfiring.