first thing I would check would be to make sure the lift pump is running. turn the key to run and see if you can hear it. it is going to be next to the fuel filter houseing in the engine bay. I know this engine is electrical, so another thing you might want to do is unplug each connector you can find and plug them back in. you might have gotten a plug that didnt seat right when the new pump was installed. another way to check the lift pump is to hook a pressure gage to it. 15 or so PSI idle, 8-10 psi cruseing. and no less than 2-5 PSI full throttle.
if that isnt it, it could be you might have an intake air leak somewhere. I would say somewhere around the intercooler. only way to tell is to get a pressure gage, hook it up on the intake and drive around and see what it does.
at 50mph, 6th gear slight acceleration I'm pushing about 10-15 PSI if I bury my foot in it I'll peg the gage out at 35psi.
if you are looseing intake pressure you will notice excessive smoke out of the tail pipe.
hope this helps your Cummins out