Fuel System Head Scratcher

Okay so to begin with the truck is a 1996 FLD classic with a Cat 3406EK motor. I bought the truck about three weeks ago and on my first run I was having a pretty serious fuel problem. It was sputtering and losing all power then surge back to life and do that until it died. I pulled the filter on the outer fuel rail and it was full of trash. I changed it and all was good for a while, then it did it again about 500 miles later and I threw on another filter and was good to go for about 1500 miles. Last night it did it again in Florida and I stopped on the turnpike and changed the filter and it took off but almost immediately lost all power and would idle fine but wouldnt let me shift through the low gears. I pulled over and waited 5 minutes and took off very slowly and it started it again but as soon as I got in the high side of the gears it quit and ran fine. I was under half a tank of fuel so I babied it to a fuel point and filled it all the way with fuel and it ran then with no hesitation or loss of power. I made it 360 miles, hit traffic and came to a stop, when I went to take off again, same thing it would start accelerating and then all power was gone, even with pedal to the floor, then after about 4 seconds it would surge like its getting fuel again and then quickly lose all power again. I got it up to speed slowly and then it ran fine in the top gears. I stopped and filled fully back up and it ran fine for another 350 miles. I stopped and filled up yet again but this time only 8 miles after completely filling with fuel it is doing this all over again. Both the fuel filters were replaced this morning and were both filled with fuel prior to installing them. I am at a loss and any help would be appreciated.

 

I made sure that the o-rings were in place when I replaced the filters. I was thinking maybe it was a pickup tube issue except that the pickup tube goes in the at the back side of the tank in the middle of the tank and both tanks are slap full of fuel. So even if the pickup tube fell off the opening is submerged and could still pull fuel. I looked at the lines and I dont see where anything is cut or leaking, so I'm thinking somehow the lines have air trapped in them or the pump is failing.