The supercoupe engine itself is stronger then our engines internally. They have steel cranks and forged pistons, the valve springs are stronger, ect. Which will work in your 3.8 mustang if you didnt swap out the whole motor.
You can supercharge a 3.8 mustang and produce good numbers from it. If anything, add the pistons and crank from the super coupe, upgrade the valves, springs, rods, heads, lifters and get a good cam in it, along with a supercharger and you will have a reliable 3.8 producing well into the 300 hp range. I recommend using a supercharger from either Vortech or Procharger, the Supercoupe charger will take some good modification to work with your application.
Check out the latest issue of MM&FF(December02), there are a few running in the 12 and 13 second range easily. Dan, Pete and clint are frequent posters at 3.8mustang.com and v6power.net, i think they can give you valuable information on what set-up you might want. They are the ones leading the way for all of us v6 guys right now. Depending on how the car is set up, running stock 94-98 Cobra's will not be an issue with your v6. I know about 30 cars right now, including my own that are in the low 13 second range. So it can be done. Dont let those v8 guys tell you different, cuz a fast car is a fast car. And let me tell you, the v8's are a dime a dozen, there are by far fewer v6's that you hear about running 12/13 sec quarters. It will cost us alot more, but the fact that a v6 spanked a v8 down the track is well worth it. And one that is N/A in the high 13's, Gaston Teran, the admin for v6power.net is producing numbers that stock 2002 GT's cant touch. Were talking N/A now, as far as reliability issues, we'll see how the car holds up.
Hope i gave you some insight and some direction where to go for help. We take pride in our v6 motors and so should you. V8 guys like to play big brother, but sometimes....little brother is the one whooping some ***.

__________________
Brian
-1998 Ford Contour SVT #1199 of 6535
Bat y-pipe, Magnaflow Exhaust, MSDS headers, Bat intake tube, DMD, P/S & Alt Underdrives, Pro-M 75 mm MAF, K&N filter, Diablosport "tuned" Chip, Centerforce clutch, B&M short throw shifter and some suspension mods
http://www.3.8mustang.com/forum/atta...chmentid=24993
-Former Car: 1995 Ford Mustang
To many mods to list here..lost the car to Hurricane Isabel 9/18/03
http://www.3.8mustang.com/forum/atta...chmentid=23621