Exactly what I'm thinking. Who trades in a built Shelby? Likely someone who already knows it's on its last legs and just wants to be done with it.
OP, are you sure the VW dealership took it as a trade-in, and didn't just pick it up from auction like most other dealerships? Hopefully you don't get stuck with a jacked up vehicle at your own expense.
It doesn't look like the engine was "built", it looks like the original owner had JDM put a Whipple 3.4 on a stock rotating assembly.