Like VibrantRedGT said, the computer is really nasty on the 94-95. Depending on your budget, if you want to go cheap, you can get away with a GT40 head and intake swap without hassle from the computer for the most part for a pretty fun upgrade. The iron e7 heads on the GT are the major bottleneck. Switch to GT40 heads + intake and you will pretty much have a 94-95 cobra at this point. (And, from what I have read, the stock 94-95 cobra cam is in fact inferior to the stock GT HO cam for emissions purposes) Rear end gear set swap to 3.73 or 4.10 (auto) is also a huge kick in the pants upgrade.
Depending how far you want to take this car- knowing what I know now, if i started all over on my 95, the first thing I would have done is a simple swap of the throttle setup to a fox body style cable and air intake and upper manifold (easily done if you do GT40) so I can use those parts instead. Fox parts are easier to find (especially used) and sometimes cheaper. Aftermarket taller valve covers are easier to fit from here too.
Handling- to start, switching to good street shocks/struts like Tokico HP Blues and Ebiach springs will be a big help. Adjustables are even better. Make sure you get 86-93 shocks for the rears to compensate for the shorter springs.