I have a 94' GT, and the only thing that has gone wrong was the throwout bearing and the stator in the distributor. The first thing I did to mine was just gut the cats and weld it back together. That alone made a huge difference.
As you can guess I opted to get headers, an x-pipe (no cats), and a turn down kit soon after. I noticably picked up a lot more top-end. Definately where it was needed. In my opinion, they're not much slower than fox cars. Plus they look way better. Plus if you really think its that much slower, come time to rebuild, just buy a carburated crate motor and have at it. The one thing Ford messed up on is the trans and the gearing. We needed a 6 speed and more gear a long time ago. Other than that I love my car.