Chris the B8 3.0 TDI has a twin plate 228mm clutch and is good for 800Nm plus, there is as far as I know no upgraded clutch option available. some of the europeans have managed to get 400bhp and 850Nm but at 850Nm the clutch was slipping.
To get that power he was running a hybrid turbo , very large intercooler, water /meth, serious remap, 3 inch full exhaust including 3 inch downpipe, extra fuel pump and a few other small tweaks.
Fuelling limitations with the standard injectors/ pump mean that 400 bhp is about the max without spending a lot of money.
You can make the standard car pretty quick with a remap, intercooler some exhaust tweaks mine is running around 320bhp and 715Nm of torque.
As for the gearbox i only ever looked for a manual. Never owned an auto, They don't handle the torque as well, I don't think they can take the same torque as the manual box, and even if they could I am not sure they would be as reliable.
Karl