The 5.0 Cobras are nice cars but it'll take a lot of bolt-ons to get it to what a lightly modded 4.6 will do. One thing that will give the 4.6 DOHC the feeling of being less torquey has a lot to do with how much smoother the 32 valve is...even running up toward the redline. Plus, when talking about stock or nearly stock, the newer Cobra feels incredible after you pass 4000 RPM...especially if you're used to a 5.0 OHV or a 4.6 SOHC.
I never had a 96-98 Cobra, but I have the 01 and had a 95 Cobra a few years ago and personally I'd say unless you're looking for a driveway project and want speed, go with the 4.6 in this day and age.
Incidently however, you will get the 13 inch Cobra brakes on either and the 94-95 Cobras had some distinct styling characteristics than the 96-98. Basically, the 5.0 Cobras had a plain hood, but more aggressive rear spoiler and the 5.0 Cobras have the horizontal taillights while the 96-98s have the vertical. The wheels basically stayed the same style from 94-97 (98s were completely different modeled after the 95 Rs). The main differences in the wheels for the 5.0 Cobras were they were completely polished and the 96-97 had grey trim in the recessed parts of the five spokes.