Cobra, 5.0 or 4.6

5.0's are easier/cheaper to work on and modify than 4.6's, and a little more torquey "feeling" (not actually more torquey)

But the 4.6 is simply a superior motor, light years ahead technologically, has more hp potential, has an unstoppable 7000 rpm redline, and has over time been proven to be as tough and reliable as even the old 5.0's. Plus, they absolutely love boost.

A properly geared (4.10) 4V 4.6 is a hella motor.

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.

Basically with Cobras, the newer the engine the better ('99's may be the exception).

My vote goes for the 4.6 4v, I use to have a 95 GT, and the 4.6 is a lot more fun to drive with the 4.10s out back.

Cobras love gears 4.10+ I haven't seen a 5L at the track running the same times as me or even close with still running stock longblock. DOHC all the way. -Mark

all i know is that i have had my 95 gt 5.0L for about 2 years and i've added little things here and there (check sig)

dont get me wrong i love my car...but i have decided to part with my car for the 4.6 DOHC 96-98 body style cobra

4.6 DOHC
sound amazing w/ some shorties, o/r x, and some flows
good hp from bolt ons
32 valves
96-98 cobra body style---hands down the best looking stock mustang

PLUS ITS NOT A GT LIKE A MILLION PEOPLE HAVE AROUND YOU ITS A COBRA!!!

solve all your problems.... Buy a 03 or 04. Lots of power stock and scary power with a few mods. The forged internals and iron block are the way to go. With just a few mods you can push 450-500 hp easy. To get that out of a older cobra you will have really mod it a lot and lose a lot of engine life.

4.6 4V....period.