Engine rebuilt, finally

[Sasquatch]

Hello there, Oh Great and Wise Council,
Well I am finally back up and running. It only took me 3 months of pain and anguish to get through all the B/S of working with my bank to get my engine rebuilt.. and get the truck back. And I am afraid that so.e corners may have been cut, but the guys that the bank made me use, keep telling me they did the job I wanted, and used all cummins, oem materials. They claim they replaced my oil pump, water pump, fuel pump, as well. I am afraid that they messed with my ecm, because all of the error messages in regards to the dpf pressure, egt, and dosed valve have returned to my dash readout. And when the truck is idling, periodically reves up to 1100 rpms, for a few seconds, and then returns to normal idle, as if it's trying to do a forced Regen. Engine runs fantastic most of the time, and I seem to be getting g great fuel mileage, feels real strong, but I have a strange shudder, or cavitation occasionally when I ease off the accelerator and then reapply it when I'm maneuvering in traffic on the highway. Is this a sign that my damper may be bad? They replaced universal jojoints, and king pins already while they had it.
If they flashed or messed with my ecm, and I have had the mandate done, would that possibly cause timing issues, with a mandated engine, and an ecm trying to run with all the dpf, and egr stuff? Could that cause this hesitation and vibration that I'm feeling?
I would appreciate any input, you guys may have,