Here is what the service manual (2000) states could be causing your problem,
Fuel injector malfunctioning - A DTC should have been set.
Fuel injector hold-downs loose. - Torque to spec.
Fuel injector protrusion not correct - Check washer shim at bottom of fuel injector for correct thickness.
Fuel injector pump malfunctioning - A DTC should have been set.
Fuel supply restriction to transfer pump - Pressure test the fuel transfer pump.
Fuel transfer pump malfunctioning - A DTC should have been set.
Intake/Exhaust valve adjustment not correct (too tight) - adjust valves
Intake manifold air temperature sensor malfuncioning - A DTC should of been set.
Intake maniflod heater circuit not functioning correctly in cold weather - A DTC should have been set also check heater elements for correct operation.
Intake manifold heater elements not functioning correctly in cold weather - A diagnostic trouble code will not be set if heater elements are malfunctioning.
Internal engine damage (scuffed cylinder) - Analyze engine oil and inspect oil filter to locate area of probable damage.
Static timing incorrect - A DTC should have been set.
Thats all of them. I would first check and see if any codes were set. Then check fuel pressure, you know go from the easiest to the hardest. If there is a Cummins place around go there. If you are still under warranty take to DC it should be covered. Good luck.