The TDI input shaft is different from the vanagon one. That is why you need the WBX (waterboxer - gas vanagon) disc which will fit the TDI flywheel and pressure plate.
You don't need to remove the tabs, just tap them down flush; you'll see it once you get it in your hands. While minor, it would create a slight imbalance in the PP if you grind them off.The bellhouse clearancing is also minor, just hold the flywheel in roughly where it resides and you'll see where it could interfere. You'll also need to take off a few mm's from the gear end of the starter... I can't remember exactly where; the tip or the flat edge, it will be apparent when you dry-fit the motor.
Where would one find this pilot bearing? Is it a common part or custom made?
I looked in my spare parts bin and it is quite obvious why the WBX PP will not work with the TDI flywheel. The depth of the friction surface from the surface that the PP bolts to is twice as deep on the WBX, approx. 25mm vs 12.5mm on the TDI flywheel.