I have done a couple injector swaps and I have never had one with any air in it after running for just a few minutes. I would doubt that is what it is. You could have a leak, and it could be internal to the head. I would definately get an oil analysis after about 1000 miles on it even if you cannot see any fuel contamination. It could also be a bad injector.
I would go out and warm it fully. Then loosen slightly 1 injector line at a time with it shut off. Start it and see if the problem gets worse or not. Do them all, loosen when it is off and DO NOT get close to the injection lines when it is running. It can and will inject you with fuel, possibly even killing you. If you find that one line does not affect the engine smoothness as much as the others then at least you know hle the problem is on. Then I would contact DD and see what they want to do. The above is going to make a pretty good mess on the engine and driveway. Some cardboard will take care of the driveway problem, and simple green will take the fuel right off the engine and any that may have gotten on the driveway too.
If you don't want to troubleshoot extensively on your own call DD and talk to them. They have enough injectors out there that odds are they know what your problem is.