I second snicklas's suggestion that your fuel problem may be in the fuel tank selector valve. A couple years ago I was driving my truck and ran out of fuel with a 1/4 tank still showing on my gauge. I switched over to the rear tank and the truck sputtered a little and stopped and I had 3/4 of a tank in the rear. So I figured it was the filter or the mechanical fuel pump. After replacing both it turned out to be the fuel tank selector valve had become clogged with pieces from the broken fuel tank pickup and I couldn't get enough fuel from either tank to make the truck run.
I put in a new selector valve and have had no more fuel problems other than having to keep the front tank above 1/4 full. You could temporally bypass the selector valve and run off one good tank until you put in a new selector valve. That is if it turns out to be the problem.
Bye the way if you end up replacing your selector valve with a universal fit selector valve that has the hose barbs and not the Ford quick connectors you can cut down these fuel line repair tubes that will fit your quick connections and then clamp a short piece of hose on it and the barb fittings on the valve.
I put in a new selector valve and have had no more fuel problems other than having to keep the front tank above 1/4 full. You could temporally bypass the selector valve and run off one good tank until you put in a new selector valve. That is if it turns out to be the problem.
Bye the way if you end up replacing your selector valve with a universal fit selector valve that has the hose barbs and not the Ford quick connectors you can cut down these fuel line repair tubes that will fit your quick connections and then clamp a short piece of hose on it and the barb fittings on the valve.