If I read this correctly, the car is a 96 GT and the speedometer was working correctly until the 97 COBRA transmission was installed.
The COBRA Transmission has a 7-tooth gear on the output shaft and the GT came with an 8-tooth internal speedometer gear. This will make the speedometer run fast.
What color is the gear on the tip of the VSS sending unit on the transmission?
Is it the same VSS and gear that was on it before the swap?
Or, if you know the differential ratio we can go to the charts and figure out what small gear mates with the large 7-t gear in your COBRA T-45.
1965 5.0 Coupe /MAF/EFI/Astro A-5 T-5/B303 Roller Cam
Mustang Manual Transmission Specialist