Couple of things you need to check to start with.
1. Voltage check on the FICM (Fuel Injection Control Module)
2. Fuel pressure check.
I'm no pro, and I'm sure others will chime in. I believe the FICM has to be 48 volts or higher to work properly. There is an upgrade from dealer (Blue spring upgrade kit) that raises the fuel pressure and in turn, injectors work better...and last longer.
2005 F-350 CC, LB, 4x4, Dually, 6.0 Powerstroke, Torqueshift, 4:10 Gears. Gooseneck and rear pull hitches. "Truck Covers USA" roll up aluminum tonneau cover. Putco Boss Running Boards. Aluminum finned diff covers. Bilstein HD shocks. ProComp steering stabilizer. XRF ball joints. NC Hornet CCV mod. RCD egr delete kit. AirDog fuel system. Strictly Diesel's regulated fuel and coolant return lines kits. Amsoil oil bypass (by NUC Motorsports) and homebuilt coolant bypass kits. CFM intake elbow. ARP head studs with factory gaskets and all upgrades. FICM by Ed with Atlas 40 tune, DC Power 185 amp alternator, MBRP 304SS "Cool Dual" exhaust system. SCT Livewire tuner with pyrometer. Autometer 'A' pillar gauges (Boost/Trans temp/Pyrometer/Fuel Pressure). 850 CCA Motorcraft Batteries. Using Rotella T-6 synthetic oil. Upgraded degas tank and cap. Hayes deep aluminum trans pan. GoGo Diesel modified direct clutch solenoid. Retro Solutions HID head and fog lights. High idle mod. Jimmi-Jammers. +More.