If the owner didn't receive a programmer, or there are not tuner boxes connected in the engine bay, you might want to get someone to flash it back to stock to be sure.
Anyone with a smarty (assuming they set their truck back to stock first) can plug their smarty up to your truck and put a tune on it, then put it back to stock, and assuming that there's no latent program inside and they have the latest update to their smarty, your truck gets the latest stock program.
Alternative is to take it to dodge for the same, about $100 and they will flash all the computers back to stock, not just ECM/ABS.
It would at very least tell you if it's ECM related or not... if the problem persists after that, my vote would be to pull the injectors and test them all.
That brings up another point - when y'all were doing the work on the truck, did you take the old injectors out? If so, did you use new crush washer shims when you put them back in? If not... that'd be the next place I'd look. They are a single-use item.
2007 3500 MC DRW 4x4 5.9L (122k mi)
G56 / SBC SDD3250
aFe Stg 2 / Pusher / GH Delete / FTE 5" TBE
AirDog II DF-165 (P551315/BF1275) / GDP Canister Delete / Bosch 505 - Stock Tips (Replaced @ 112,381 mi)
Autometer / JVC / Polk Audio
Best Tanks: 16.6 towing / 23.92 unloaded hwy / 23.2 city