Fuel Pump?

[NYhc416]

Had a few problems over the winter with 06 psd. Truck at the time only had around 35,000 miles. Has had 2 egrs replaced, oil cooler, and gaskets replaced. Has djs tunes (mostly run economy), 5" turbo back no cat but muffler, and zoodad mod. When driving down the road the truck starting shuttering as if running out of fuel but the tank was on a 1/4 then it cleared up. Parked the truck for about 3 hours then drove it again had no problem till about 5 miles in the truck begain to shutter again and then died out on me. I made it back home and put some fuel in it I thought maybe it was some bad fuel. After I fueld it up no problems. Now a few months later anytime I go below 1/4 tank and shut her down it misses when it starts as if it were out of fuel. I have replaced the fuel filter and also put it back to stock but still the same. Could this be the fuel pump? Injectors?. It almost seems like it looses its prime or somthing.