Depends on weight of the two cars, and gearing, traction, aerodynamic aids.

a 1991 mustang going 100 mph would EASILY overtake a 2003 mustang going 75 mph.

The 1991 might be a tad faster due to them being lighter that the later models. However, Ford really seemed to sandbag the true numbers on the 2003 for horsepower. I saw some tests before the car hit production that were pretty staggering. I remember one dyno test showed a 2003 w/ no exhaust other than stock headers pushing upwards of420 at the wheels!!!! I also know of a 03 Cobra near my hometown that is dipping into the 9′s with basically all bolt on’s. They’re pretty sick cars from the factory but so were the earlier Fox bodies.

First off “Ruskin”, the 2003 ford mustang and 2003 ford mustang cobra are absolutely not limited to 97mph from the factory. There factory limiter for the gt is set at 149mph, not 97mph. The cobras is set at 155mph.
If you put both vehicals on a dyno to make sure that they have the exact same hp, then as far as 1/4 mile times the 1991 mustang will be faster then the 2003 cobra. The 1991 mustang weighs much less then a 2003 cobra does which would give it the advantage. Now as far as top speed goes, the 2003 cobra would have a faster top speed then the 1991 ford mustang. It is geared better for higher speeds and has better aerodynamics including the front ground effects and rear spoiler which would give the 2003 cobra the down force needed to have a higher top speed then the 1991 mustang. So as far as acceleration goes, the 1991 would win, but talking top speed, the edge has to go to the cobra. Like I said in the beginning though, you would have to dyno both cars to make sure they had the same hp because the factory rating of 390hp and 390tq is very under rated for the 03/04 cobras. As anyone who has even one day of racing experiance or one day at a shop with a dyno will tell you, the 03/04 cobras make almost 390hp and 390tq to the wheels stock. I have seen close to 100 stock 03/04 cobras put on a dyno (either dyno jet or a mustang dyno with the numbers adjusted to be equal to the dyno jet), and 99% of them put the rear wheel hp and tq between 365 and 390 rwhp with the large majority being around 375rwhp. This would put the fly wheel hp (that is the hp the factory uses) at about 425hp and 425tq. So thats why you would have to make sure that the 91 stang and the 03 cobra really do have “equal HP”.