Your injection pump does not have all the elements contributing properly so there will be vibration or rough running issues. Your retarding the inecction pump to partially eliminate the severe number one cylinder knocking does not solve the issue. It just masks it somewhat.

You really should examine how to do the milli volt method of checking and adjusting the number one element that is so far off. Or grab a used injection pump from a pick and pull yard. Getting two threads going that perhaps involve the same issues adds complications.