What? That's absolutely not true.
With 3.73's at 50mph he'd be at 4800rpms in second or 3250 in 3rd gear, with stock 3.08's he'd be at 4000rpms in 2nd and 2700rpms in 3rd. Punching the car at 4800/3250 verus 4000/2700 will DEFINITELY enable the car to accelerate quicker as you are starting at an RPM where more power is made and with the added gear ratio it will get into the higher RPM's where the big power is made. Unless you are racing to 150+mph where the lower gear ratios will force a shift into 5th gear, gears will give you an advantage everytime over a stock gears. Don't forget about torque multiplication as well from gears too which also aids in acceleration.
Stock for stock the 99-up GT's will pull a few more MPH in the 1/4 than the 94-95 cobras (~98mph for the '99 and ~96mph for the 94-95 cobra) but with gears, exhaust, and an intake the cobra should pull a few more MPH than the stock 99. It would be a driver's race though on the street.
To the original poster, it goes without saying to be VERY careful that you do NOT do the 3rd to 2nd gear shift again. I did it last april and my car is still down with bent exhaust valves. You are VERY lucky if you didn't hurt something.