You may be getting into phase separation if the fuel you're burning has ethanol. Ethanol combines with water in the fuel, but only to a point. Once saturation is reached, the ethanol and water separate from the gasoline and collect at the bottom of the tank. This makes for rough running and loss of power.
I got into this with a Dodge Neon. Like you, I thought it was a fuel system problem. I was in the habit of topping off the tank when it was about half full.
The solution was to burn the fuel tank down nearly empty before refueling. Running was very rough the first time I did this. Adding some dry gas seemed to help.
After doing this a few times the car straightened out and ran fine. To keep the problem from recurring, I then held off refueling until the gauge indicated 1/8th tank remained...or the fuel warning light came on. I also added a bottle of STP fuel additive (the cheap stuff...$2.97 for 3 bottles at Walmart) at each fill up. The problem never returned.
Red candy '11 F150 XLT SCab 4WD w/5.0 V8, 3.73LS, Chrome, Convenience & Tow pkgs.