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YOu would have to swap the engine, entire wiring harness back to the ECM, the ECM itself, possibly the cluster. WIth the ECM replacement you are going to have to adapt the immobilizer to it. It's not a home job if you aren't experienced with VWs as there are always things that will come up that are unexpected.
There are two basic versions of the VR6- the 12 valve and the 24. You want to replace it with the same as you have, but should be able to pull it from any body style as they are the same. If you are dealing with a junkyard, they have a network that connects all the junkyards, so they could ship it to you from another yard. It's worth it as these engines are guaranteed to be operational, which might not be the case in a U-Pull yard.
Any A4 platform from 1999-2001 will have the 12v VR6, so any Jetta, Golf, GTI. In 2002 it upgraded to the 24v