The complexity of putting a longitudinal engine in a chassis designed exclusively for a transverse engine will require so much work and modification I wouldn't bother with the VAG V6 TDI!! I've got one in my Touareg and it's not that mind-blowing as
@Sasquatch said above!
You want to check out
DieselPumpUK and
DieselPumpUK Shop those guys are nuts with what they can put the the Mercedes-Benz OM606 engine into!! (And the power output will be mental!)
They'd be able to do it in a Transporter for sure!