The sn95 chassis has a few differences from the fox, it's stiffer, the brakes are bigger and there all 5 lug. There then that its basically the same car just much much better looking IMO.
There are 3 cobras that your going to be looking at if your shopping for one from the 90's. The 94-98 cobras come in 2 verities the 94-95/ 96-98 and then there's the 99-01.
The big differences are
94-95
look just like a v6 except for the cobra front bumper, special "crab claw" rear spoiler and there is no 3rd brake light in the trunk. Also they came with a special wheel package.
Performance wise it still has the old pushrod 302 in it,comes with iron gt40 heads,special intake manifold, 1.7 rocker arms, and a special cam. They where rated at 240hp and 285tq but most seem to dyno at around 280whp so many believe for under rated the hp.
96-98
As far as looks, it has a awesome hood, same cobra front bumper, COBRA rear bumper, different tail lights and different wheels.
performance wise your looking a DOHC 4.6 v8 rated at 305 hp and 300tq. I don't have alot of experience with this engine i'm a sbf fanso i can't commpent to much on it but it does weigh more then the sbf and they allwas seem to have more trouble at the track then there push rod counterparts.
Also both these cars are running struts up front and a SRA in the back with the same factory 4 link as the fox bodies.
99/01
The 99/01 cobras are the most unloved cobras of all, they have irs but uses the weaker 28 spline carrier and axels that snap if you even think about using an aggressive tire and going drag racing.
There rated at 320hp and 317tq but there where so many problems with the 99's when they came out that ford did a recall on them replacing the intake manifold (because of a bad batch of castings), catback exhaust and retuning the car because the power was so much lower then advertised. They then skipped the production of the 2000 model "base cobra" in the use US and re-released it again i 2001 with most of the issues sorted out.
Don't get me wrong the 99/01's are great cars there just over shaded by the mach-1,03-04 cobras and the 2000 cobra R