If you do decide to give it a go, for the gearbox mounts you could go over to Mike's and measure the factory castings, then just CNC aluminium mounts yourself, should be much cheaper than factory mounts.
Front half shafts may still be available from Audi and the rest of the shifter assembly too, worth giving them a ring to ask.
Definitely go for a A6 TDI gearbox especially the one with the .56 6th gear
I will post up codes of A6 transmissions and gear ratios later.
The pedal box mod I designed needs one small alteration to the shape of the clutch pedal, I will modify the CAD drawing soon. We tried it in a shell of a D2 at the A8 parts open day, the clutch pedal cleared all the footwell obstacles. Even the transmission bump does not need removing. Also worth asking Mike, his machinist friend may already have made the clutch pedal for him and the rest of the pedal box mod.