New approach to this topic:
With the swap to VR5 / PD130 MAF we were trying to implement two changes at the same time: MAF type (from HFM2 to HFM5) and diameter increase (from 2,5" to 2,75"). So I had the idea to go one step at the time to try and diagnose if the my problems were caused by the maf type change or the diameter change.
So I did the test with a good known 2,5" HFM5 maf from a ME7 1.8t from a collegue's car. Converted MLHFM from 512x1 to 256x1 and put the map in ecu, and the car idled as bad as with the VR5 MAF. So problem seems to come from the maf type change.
I remembered people mentioned they deleted the negative readings from the map (which I didn't trying to see if it worked out of the box, as remember, VR5 uses HFM5 MAF with M3.8.3 ecu and this has negative values in it), but so did I zeroed those values and the car now runs much better but still slowly goes back to stumbling... But it's some progress

I have seen PRJ list the maps he changed to adapt HFM5 from R32/Phaeton to M3.8.3, but he also adapted other injectors at the same time and the list is a big mix. Here it is for reference: http://nefariousmotorsports.com/forum/index.php?topic=21532.0title=
FGAT0
MLST
MLHFM
KLWF
KFMLDMX
KFLF
Cold start cranking map. IDK the name found in ASM.
TVUB
KFBAKL
KFVAKL
ABAKN
FBAWN
FVAWN
I believe the only maps related to the MAF are MLHFM and MLST, but MLST being only the initial MAF reading for startup I consider it may not be involved afterwards... I have gone through M3.8.3 damos and FR and haven't been able to see anything else that may need tweaking.
We would be very appreciated if anybody with some experience or knowledge could chime in and give us a hint on what to look at or consider relevant to keep moving forward. I belive this to be an interesting topic to all of us with AEBs, AGUs, VR6s, with the old style mafs which are stupidly expensive and hard to find, to be able to switch over to a more modern and cheaper (but yet Bosch original) component.
As always, thank you all in advance.
Best regards