Hey I know exactly what your getting at, my 2000 GT had a 97 t45 in it , my speedo wouldn't register at all. Because, the BorgWarner and tremec in 96-98 were gear driven speedos, the later model 99+ used a reluctor ring on the out put shaft and a magnet reads the rotations. Yes the rpm revving is directly related to the out put of the VSS. As a matter of fact my 2000 had the reverse problem your having. Upon releasing the accelerator, and coasting my rpms would drop and effectively create an engine brake.
There are 3 methods you can take here to remedy the situation .... I chose to put the correct trans in mine.
1. get the correct model year trans for your car.
2. Swap out the tail housing and remove the magnetic reluctor ring and replace with a gear driven , get a gear driven vehicle speed sensor. The tail housing must come from an earlier year T45 and must be swapped due to the way the sensor mounts in each.
3. Get your self a Dallas mustang speed cal
If you choose to swap the rear tail housing and speedo gear, I have a 97 borg tail housing and gear drive for it , it might even still have the VSS in it for that year. PM me if your interested in purchasing it. Id make ya a good deal on it.