Who built your injectors?
M-TDIs are actually a lot more sensitive to injector imbalance than you might think. The combination of high pressure and a large pump plunger makes for a very short duration; unbalanced injectors can be a bit more apparent than on an IDI motor. Actual electronic TDIs have injector compensation in the pump controlled by the ECU and are slightly more tolerant of mismatched injectors.
To see if you are in fact running on 3 cyls try loosening off the injector lines one by one with the engine running, you should have the revs drop as the injector stops firing. This is like yanking the spark plug wire one cylinder at a time on a gasser to see if one isn't firing - if you find one where there's no change in how the engine is running when you loosen up the line you've found your culprit.
Puff of black on startup is normal. Some versions of the LR300 pump had a linkage that would reduce fueling in this scenario - I had that version and removed it to get the top back on my pump easier then discovered just how much it had been helping. I have a pretty scary cloud at startup...
The mechanical pumps go to full fueling until the flyweights in the pump spin fast enough to kick the governor lever back over which is what causes the startup smoke.
Finally around idle speed, the factory idle speed is apparently around 720RPM for some versions of the Land Rover pump, so the fact that it's trying to settle down there isn't that surprising. You may need to stretch the idle spring out a little; I actually need to do this myself. My engine is pretty smooth at 1K but shakes like crazy around 900 and lower.