1999 Ford F-150 Heavy Hesitation

I have a 1999 F150 and for the past 1 1/2 years I have been dealing with a very intermittent problem. It started acting like it was missing about 1 1/2 years ago, I changed the plugs thinking it was about time they had never been changed. This helped my problem and it seemed to go away. About 4 months later it started acting up again doing the same thing. I put another set of plugs and this time put wires on it(autozone cheapos). This seemed to fix my problem again. No problems for about 4 months. It came back same problem, feels like a miss and hesitates real bad under load, truck stutters and jerks. I went ahead and got a set of motorcraft wires and put on it. This cleared the problem up again. I thought I was in the clear but I came back again. I asked around about what else it could be since I do not think it is electrical related now. I did a complete service on my truck, oil change, filter, fuel filter, all that good stuff. Come to find out my fuel filter was very clogged, I was happy to see this since I figured this was my problem. I drove it with no problem for about 3 weeks and it has come back and it seems to be getting worse. When I mash the gas it does not seem to want to go anywhere and I am getting a slight knocking noise sounds like from the throttle body. I have talked to a few people and they say it could be my fuel pump going bad. I have checked the fuel pressure and it seems ok but this might be a volume problem. Any help would be appreciated.