Hi,
To keep you on track with this worthwhile project - some info , firstly the original 3pin coil is 1. Live supply from the ignition relays , 2. Ground , this is in the harness to the chassis , 3. ECU switching . The 4 pin audi coil is 1. Live supply , 2.Ground - in harness to earth point, 3.ECU switching , 4.Ground - directly to engine block.
It seems possible to replace the loom connector [1J0 973 724 reqd] , but removing the pins from the old connectors without damaging the securing lugs ( difficult even with the tool ) and then I suspect not compatible with the vag connector. I would suggest buying the loom section for each bank , which seems good value compared to the cost of 12 3pin coils making this more of a plug and play exercise. keep up the good work