Sounds like the egr but seeing as you didnt get the regen taken out it could be the software. I personally dont think it will try to regen if it isnt there but that is an educated guess. It wont see a delta P.
I have had mine hiccup after I had the inlet manifold apart and it was the egr. I cant remember how I fixed it as I have done so much to the car you tend to forget. Get them to map it out and give it a try then egr.