It's been done by a few people including myself. As said above, your stock 3.8 probably won't last long because of the stress the M90 will add to your stock pistons and head gaskets.
You'd be much better off if you could swap the complete Supercoupe engine instead of putting the Supercoupe stuff on the N/A 3.8 engine. If you did decide to use the stock N/A 3.8 as 2 people I know have done, you basically need to swap everything from the long block up. All accessory brackets, pullies and tensioners, manifold, fuel rail and rig up the SC intercooler.
You use the Mustang ECU and tune it with a chip or flash the computer.
There's plenty of info at - V6Power.net