Cm870 vibration concerns

[Precisionw900]

So I have confirmed no air in fuel system. Ran a leak down and cutout test. Passed and will run on 1 cylinder all sound the same. Still runs rough at start up for 10-30 seconds.
As I said before my local Cummins dealer was supposed to make sure a factory tune was installed due to an add on after treatment system that was removed from truck. ( ex Cali truck) mechanically it checks out so could they have screwed up installing factory tune? It has horrible throttle response and very sluggish rev. Just want to be sure I shouldn’t be looking for something else before i waste time tuning.