The term 'handling' is such a subjective one - it's really difficult to nail down exactly what good or bad handling is. If you drive a 30 year old pickup truck day in and out, and hop in your SN95 on the weekends, relatively speaking - it handles unbelievably well. On the other hand, if you've, for example, been an amateur or professional road racer, and driven race prepared vehicles - then hop in your stock SN95 - well, it probably doesn't feel like it handles so well. It simply doesn't make a lot of sense to try and describe it from a good, bad or even better handling perspective. It's more complex and subjective than that.
The other issue that bears discussing is the driver's role in all this. With a really good driver, I suspect we'd all be amazed at how quickly many unsuspecting cars can be made to get around an autocross or road course. A really gifted/well trained driver in a car that doesn't handle that 'well' can absolutely embarrass a less skilled driver in a very good handling car. So comparing lap times between cars really doesn't tell you much of anything. Put the same less-skilled driver in each car and then compare times - that tells you a little bit more about what's going on with the vehicle. Put the same skilled/well trained driver in each car - then you can really get a feel for the car's capabilities. To put that in the context of this discussion - a very skilled driver in a stock Fox body could run all over a less skilled driver in an SN95.
Ford evolved the car through the years. The changes for the SN94/95 cars were aimed largely at making the car more sophisticated (less NVH), better at stopping and better handling. A MUCH stiffer unibody was key to achieving reductions in NVH and to having the car handle better, and that's what the SN94/95 got. Even though it's a bit heavier, it has the potential to be better handling. Whether it lives up to it or not, in comparison to any other vehicle is largely in the hands of the driver. And when you start trying to compare modded versions of either car (Fox/Sn94-95) all bets are off.
There are lots of ways to improve things - y'all know the usual suspects out there that have proven suspension/chassis stiffening kits that help the Stangs handle better/more predictably. But the single biggest handling challenge for Fox or SN94/95 Stangs is difficult to overcome. It's the placement of the engine so far forward in the chassis - and the resulting forward biased weight distribution - it impacts handling and braking performance. If you take a look at the world-class handling vehicles out there - you'll almost always find that 1) they are mid-engined or 2) if front-engined, the engines are significantly set back in the chassis. Look at the tube-framed Mustang and Camaro TransAm cars from a few years back. The engines sit nearly under the windshield, and the driver's almost in the back seat. So if you really want to shake things up - cut that firewall and move the engine/tranny back. And then get ready to come up with your own spring/shock/bar rates and suspension geometry -- because nothing marketed for the Stang is designed with that static weight distribution in mind. Or you could always try to engineer an awd system -- anyone watch the Audis kick Cadillac/Corvette/BMW/Porsche-butt at Road America this weekend? Yeah I know - they keep adding/subtracting weight to equalize things - but the awd cars ALWAYS win the standing start!