You have a lot of unknowns in your build, so until you eliminate these, you will be doing this all by trial and error. To me, questionable things:
Cam: Fit for purpose? Timed properly?
Pump: Serviced, set up and in sound working order? Timed properly?
Engine: Have you ever seen it running well? ie with original ecu'd pump and cam? Compression tested? Injectors known to be happy?
When you say you got the TDC from the landy unit what do you mean? Timing is obviously ALMOST there, or you wouldnt be running at all. By the sound of it you dont have a good TDC mark to start from.
Also, if you've been messing with the pump to compensate, even when you hit perfect timing (which you may have already) the engine will not run well. I worried this is half of the problem.
First off for me would be
1) ensure that your TDC mark is sound (this was my first stumbling block as my engine is in a van now, and the bellhousing mark was different to the golf bellhousing the engine came from!) If it isnt right, your cam may be out too, and that will mess up running.
2) find out for sure that the aaz cam is happy in a tdi. even if it is, swapping a standard tdi cam back in will eliminate one less potential issue.
3) if you have messed with the different settings on the pump, return them to standard (if you marked everything up) or take it to a good pump shop and let them do it (see if they'll do the gov mod for you while its open!) Remember, theres only so much people like us can do with these pumps, guys dont invest years and thousands in training, experience, and equipment for fun. Its specialist stuff, that we can destroy in 5 minutes in our sheds!
Keep us up to date, I love the concept of mtdi-ing these engines, and want to see you get this sorted.
mm