Michael
I would crack an injector line one at a time and try and find out which cylinder it is. Then swap the injector and see if the bad cylinder follows the injector. When its warmed up is it still rough?

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1985 Euro 240D 5 spd 140K
1979 240D 5 spd, 40K on engine rebuild
1994 Dodge/Cummins, 5 spd, 121K
1964 Allice Chalmers D15 tractor
2014 Kubota L3800 tractor
1964 VW bug

"Lifes too short to drive a boring car"