The 96-98's have about 40 more rwhp, and are faster stock vs stock. The 94-95's have more down low and off the line, but the 32v 4.6's will catch and pass the 5.0 in the 1/4. The 94-95 cobra might loose and have a slightly better 60ft time.
No they don't run about the same. I know I own one. The 94-95's are a lil slower apx. 30-40 rwhp slower. The 96-98 don't have as much low end grunt as stated above and the 94-95 have more low end torque. The 96-98's have the wicked power on top and pull really hard in the upper rpm's. In all the cars can both be modded to hell and back. The 96-98 dohc mod. V-8 block and internals will hold up to more mods. and higher hp. While the 5.0L are known for daily drivers lasting 200k miles or more with correct matience.
stock with good driver in each car a 96-98 will outrun 94-95 in the 1/4. As far as the 1/8 goes its really close but usually the mod. motor ends up on top.