Did you read the information the T45 tail shaft swap?
The VSS sensor has a GEAR on the end.
The OSS sensor has a MAGNET on the end.
As stated before the output of the two sensors are not compatible to each other. The sensor type needs to match the tailshaft, transmission harness, and PCM. Therefore, if a VSS wiring harness is mixed to a OSS style PCM, you can expect problems.
The only way I know how to tell the wiring harness difference is by comparing the wiring colors to the wiring diagrams.
Try researching extended range SpeedCal. However, I'm not sure it will work with a 1999+ MY. However using the correct sensor for your model year will give the greatest chance of success IMO.
2003 GT Convertible (sold)
2000 GT coupe (Craigslist project. Fixed. Now my DD). Windsor to Romeo swap.