Muscle mustangs and fast fords put a vortec supercharger on a 99 3.8 mustang and got 260 rear wheel hp. (faster than a stock gt) I'd say the supercharger is the best mod for your money hp wise. A good exhaust wouldn't hurt either.
I have a 90 supercoupe that came from the factory with the 3.8 supercharged motor(not the 4cyl turbo)its one quick little car. it will go way to fast on the top end also(pretty darn near 150 mph car with a 5 speed and 2:73 rear) Lots of fun . Wife makes me store it now so i dont get in trouble
I too have an 89 Super Coupe auto. It is very deceptive just how fast these cars are. It is no trick at all to go well over 140. Some have a gov. that is easily defeated. They handle very well stock and supurb when tricked up a little. The only real sad part about the SC is it is so *&%$# expensive to maintain. these cars are probably the fastest stock US sedans to hit the road. Not only fast but most get 25 mpg hwy or better.
If you go the supercharger way (best as noted above) be prepared to put head gaskets in every so often as this motor has a habit of schucking them. Even the Winstar van does. You will need a much larger exhaust system to go with it or you will most definitely blow HG.
Go to the Super Coupe Club Of America (SCCOA.com) for the most comprehensive auto specialty web site in the world. Everything that has ever happened to a 89 to 97 t-bird has been hashed over many times. Lots of neat people too. There are a lot of SC only events all over the country listed too. The t-bird is one of the most under rated cars ever made. Ford screwed up this one. You can make yours into one handling sob very easily (ie by spending a >> sum of cash)too.