hesitating

I have a 2003 F-150 with a 4.2. I ran out of gas not too long ago and ever since the truck has been hesitating and jerking between certain rpm ranges. 2000-3500. anything below or above if fine and constant speed is fine too. Its only in acceleration that I have the hesitation. My first guess was dirty fuel line, so i bought a new in-line fuel filter. didn't do any good. next guess would be injectors or fuel pump in the tank, but before i do all that I was wondering if anyone had any other suggestions, or has had this problem before and knows exactly what to do.

Have the truck scanned. These trucks are notorious for bad COP's. (That is Coil over Plug)