I have a superchips programmer on my truck whenever I go over 2000 rpms it cuts out for second then comes back sometimes cuts out and there is loss of power till I left of throttle and go back into it .... But if I take my superchips programmer and put the truck to stock there is a loss of power barley revs up likes it's in limp mode

 

got code P0216 and P1693......is it the pump ? - Dodge Cummins Diesel Forum
This might help in your diagnosis. If you have what they are talking about its not looking pretty.