I wouldn't have thought standalone ecu would be necessary (or worth it), just get the immobiliser parts removed from the OEM one with a reflash.
Mounting points on the engines are different, but all the brackets currently on the mk3 should bolt onto the 3.6 block to make it compatible with your engine bay - I'm assuming the passenger side rear bracket holes are there as they were in my mk4 motor.
Nice that you've already got a vr6 gearbox to work with too!
So physically it should be straightforward, but I'm not sure about the electrics.
You'll be going to a drive by wire throttle, but it is so good that you've got the Passat there to plunder parts from.
Which gearbox was in the Passat?
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