One of the problems here is I don't believe that you understand WHY the V6 Mustang has a speed limiter in the first place. It has to do with the "critical speed" of the drive line (U-joints, drive shaft, pinion, and slip yoke). The Ford engineers set the max speed to keep the drive shaft itself from spinning faster than it's "critical speed". So when going to a lower rear end gear and keeping the same drive line, the car's top speed will need to be lowered in order to stay below the "critical" speed of the drive line.
Regarding trouble shooting the VSS sensor. The VSS sensor generates a saw tooth wave form when turned. If this were my car I would start by CONFIRMING a good ground on the VSS PK/O wire.
Next disconnect the VSS connector and put a Volt-Ohm meter (VOM) on the VSS sensor. Put the car on axle stands and disable traction control (if equipped). Spin the wheels and MEASURE the output of the VSS senor using the VOM set to the AC scale. What the reading is will depend upon the VOM meter. What we are just trying to do is a basic functional test to confirm that the VSS is generating ANY signal. You should also see a change when the wheels spin faster.
IF the VSS is not generating any voltage then first suspect that either the plastic gear on the VSS has worn down or the worm gear on the transmission output shaft has worn down. You should be able to see the transmission output shaft worm gear once the VSS sensor has been removed.
Note for cars with a VSS sensor, the sensor output goes to both the cluster AND the PCM. A bad VSS sensor would cause the speedometer and PCM to not have a good speed signal.
IMO it's far easier to use a scan tool to "ask" the PCM what the car's speed is.