The first thing I would do is run the Cummins diesel diagnostic fuel test on vehicle.
Running these tests will test transfer/lift pump flow across fuel filter, CP3 pump return flow, pressure limiting valve for leakage, and injector return flow.
These tests require special test fittings to install inline in fuel system and also require a scan tool to overide fuel pressure to boost psi to max. These tests will best to have done a Dodge or Cummins dealer.
In doing these tests they will determine if your transfer pump has the correct flow.
They will be able to verify fuel quality and determine if there is fuel contamination.
Testing the CP3 pump to verify it can actual pump the desired volume of fuel to rail.
Test the limiting valve to verify it is not leaking so fuel system can build proper psi for operation.
Test for excessive injector return flow which may be caused by leaking high pressure connector tubes at the injector socket, or internally damaged or restricted injectors.
Also, they will be able to check the engine controller for software level, as there have been many updates to software for driveability concerns.
THis is where I would start. It sounds like a fuel issue to me, and this will narrow down the concern the quickest way.
Hopefully this information is helpful. Thanks and good luck!