Are you sure its a 6-speed? According to the data and my experience the B5 1.9 TDI is a 5-speed 01A. The 01E only came with the 2.5TDI in the B5. It wasn't paired with a 1.9 until the C5 and B6 with the PD130. Also the B5 diff is different to the D2. The ideal donor is the A6 C5 2.5TDI, or possibly a B6 1.9TDI although they have odd output flanges.
I've done a swap in an S8 with a TDI 01E and its ok, not great. 6th is just a bit too high, meaning it does about 1600rpm on the motorway and while that is great for fuel consumption, having to change down to accelerate gets tedious.
You would have to have your propshaft extended since there is no LWB manual from the factory. In theory you could bolt the front of a manual shaft on to the back of a LWB shaft, but manual shafts are extremely rare. Easier to extend it if you can find someone capable of doing it.
S4 stuff does work, but you'll need the spacer between engine and gearbox which will also impact the propshaft. TTV Racing in the UK make a flywheel to take a B5 RS4 clutch which doesn't need the spacer - that's what I've used in the past, and the RS4 clutch is quite cheap. Get the heavy flywheel if you go this route.
The only other thing to bear in mind is that you'll need an S8 manual map in the ECU since there is no manual map for the A8 4.2. This means also swapping to the S8 inlet manifold and throttle body, injectors, and airflow meter so the ECU knows what is going on.
