Truck Repair: 1998 signature 600, cummins quickserve, fuel mileage

Question
have a little problem
check engine light goes on, engine starts to run rough almost like its missing (but new injectors)
i found filter screen on that big ifmc or somthing or other and replaced it. took to dealer and they said its a fuel obstruction because its reading low fuel pressure. has a electric transfer pump (maybe aftermarket)
i found on cummins quickserve that it has two pressure regulator valves, can those be it? what can it be? only does it sometimes and sometimes it runs like a charm. if the light goes on the fuel mileage goes down the shitter. maybe another filter screen in that mess or a solenoid? and if it is it the metering or the timing? way to test them? maybe injection pump? please help!

Answer
If you have not replaced the gear pump(fuel pump on top of IFSM) on the IFSM I would recommend it & the pressure sensor.Also have it checked for the unintended fuel pressure sensors(located on the bottom rear of the IFSM).There are 2 of them & they have a kit to remove them from the system & get it recalibrated to the latest updated code.