Sounds more like the sequential timing of the injection pump is badly off for the number two cylinder or the injector is bad. You have eliminated the injector as a source.

Smoother sounding with the cylinder disabled is the indicator of this. I was also trying to figure out another possible cause but it is not happening. What I would be looking for is an indication that the cylinder is indeed running hotter by the milli volt method first of all. If it is. Mark the element positon well for a refferance point to return it to and try adjusting the element.

I would use the mili volt method as I suspect that cylinder is running very hot by injecting early. Without using the milli vots you would not be certain of that. That also is good in a strange way if so because it means the element for that cylinder is still capable of reaching pop off pressure. In a situation as severe as yours making the voltage from two new glow plugs the same by adjusting the element on the number two should be a major improvement. Remember to mark the start position of the element you are going to adjust though.

I also would not drive that engine as is too much. We have never had a hole burnt in a piston yet to the best of my knowledge. When you had the injector out did you look at the pre chamber? The symptoms are wrong to me for a camshaft or valving issue is my feeling. I could see the white smoke if the injection was extremely late but the engine would not run rougher with the injector on line.

One last thought would be to look at the camshaft lobes etc for that cylinder first though. I suspect they are okay and on average would not cause your symptom yet it never hurts to check. I also realise there are repeat issues in getting the delivery valve operating properly on this models pumps. It just strikes me that early injection on a cylinder is not one of them but truthfully I do not know.

What am pretty positive of and it is a good thing. Is the internals of the engine for that cylinder are probably with a certain amount of good fortune not the issue. The white smoke with the cylinder activated although an indication of something I would forget until I saw what the milli volts are indicating. Although the presence of it is troubling. If the cylinder is running colder than the others do not adjust the number two injection pump element.