I have done a LOT of research regarding putting a SuperCoupe setup in a Mustang. From everything I've gathered, the #1 BEST option is to swap the entire engine from the S/C to the 'stang, rather than trying to make the M90 Supercharger work on your existing engine. The S/C 3.8 has a lot of "beefed up" internals to help handle the 12psi boost the M90 puts out, plus everything is already set up to work with it. Using an older 3.8 will sometimes require different heads to mate properly with the S/C's intake manifold, plus the engine internals aren't designed to handle boost.
If you find a complete S/C 3.8 (or entire parts car) I say go for it. It's not a difficult swap, just time consuming. I was looking into doing this with the '98 I just got, but changed my mind in favor of a 5.0 (which requires about the same work, but has higher potential).
As far as fuel mileage, the S/C cars got around 26 highway, but the Mustang is a lighter car. You will probably wind up with at least that, if not a couple MPG higher (assuming the engine is tuned properly and in good working order).
If you do put a S/C engine in your car, I can't emphasize enough that you NEED a good exhaust system on your car. The stock setup will pretty much guarantee you will blow a head gasket, or worse. Exhaust isn't too expensive for these cars, and is definitely worth it to keep from having trouble farther down the road.
*as a side note, there are a lot of aftermarket parts for the S/C engines that will increase power output, but you must be careful when using them... The overdrive supercharger pulleys are the easiest upgrade, but as I stated before you MUST have a good exhaust system or you will damage your engine. If you run true-duals, and no other upgrades, you can get by with a 5% overdrive pulley for the blower, but anything higher and you're taking your chances...
Another upgrade that will help out is a larger "big-bore throat" assembly. These can be found here...
http://supercoupeperformance.com/partBrowser.aspx?partId=95 and are an inexpensive way to get more power out of your M90 setup.
There are a lot of upgrades for the S/C Thunderbirds that can interchange with your Mustang if you do your research and make sure of the proper fit. Good luck with your project!*