Do you have the full return-less fuel system from a the car you pulled the engine from? You'll need the stock fuel rail pressure sensor, fuel pump driver module and fuel pump for the stock ECU to attempt to make it work. The return-less fuel system is usually a big hang up for people because then you have to either modify the exiting tank/lines, or put in a fuel cell and modify that and the lines (more $).
Also, has this shop done this before successfully? I would question them and make sure they have actually done this full conversion before and know all the in's and out's to getting the stock ECU to work. The fact they quoted you $300 to do the tune makes me question that. I know people have successfully got the stock ecu to work on an s197 3-valve, but they were able to re-pin the stock 3-valve harness and use the existing body modules (and existing returnless fuel system) to get it all to work. A fox is a lot more work since it has none of that. You just want to make sure you don't waste $300 and have a brick sitting in your driveway after having everything swapped over.
You can definitely do the swap on the "cheaper" side if you do all the work yourself, but don't be surprised if your costs start to snowball at the end.