Negative.

Only 2 things can change the speedo accuracy on 96 - 98 Mustangs.
1: The rear gear was swapped to something different.
or
2: Either the speedo gear in the sending unit was changed (Highly unlikely) or the transmission was swapped to a Cobra version of the T45 which has the 7T internal gear (Also highly unlikely because the Cobra T45 uses a different cross member mounting location). The GT specific T45 has the cross member mount closer to the case. The Cobra version is on the end of the tail shaft. It either works or it doesnt work. There is no in between where it can give improper speedo readings.

The only way to alter the speedo calibration electronically on the 96 - 98 cars is with an aftermarket module like the Dallas Speedcal. It steps in between the gauge cluster and the vehicle speed sensor. You tell it what tooth gear is inside the transmission, what tooth gear is on the sending unit, then tell it what gear ratio is in the rear end and tell it what tire size is on the rear of the car and it then properly calibrates the speedo.

The clutch has nothing to do with how the speedo works. There is a speed sensor on the left (driver side) side of the transmission. It has a mechanical gear inside of it and then sends an electronic signal to a PCB in the gauge cluster. The manual transmission wiring harness performs only 3 functions. Plugs into the front and rear O2's, plugs into the reverse signal indicator and plugs into the vehicle speed sensor (The sending unit).

Hurst