Well I didn't want to pour pessimism all over your excitement, but I thought fitting a new engine would be tricky somewhere, with the ecu & stuff.
I would feel happier with a vw dealer taking responsibility for setting the car up properly.
They might fill in your service book saying a new engine was fitted? which would be great when you come to sell it...
Do you need to get the engine number changed on DVLA owners doc?
I think you need to try and relax, and let them take the time to set the car up properly