In 1999, Ford switched from a VSS sensor to an OSS sensor. Along the way, Ford attempted to standardize accross their product line on the number of teeth on the OSS sensor. I do not know the exact years that the # of teeth were changed.
Is it possible that the number of teeth on the OSS sensor is different between the 1999 MY and 2001 MY? If so, this may account for the difference.
I recall reading posts where the differences in the number of teeth can be corrected with a custom tune.
However, it would seam to me that it would be possble to "lie" to the PCM about the true rear-end ratio (or tire height) and correct the # of teeth problem. To do this, it will be necessary to know EXACT how much the speedo is off. Just saying 10 MPH wont do it.
Determine how much the speedo is off at various constant MPH's. Or drive the car at a constant 60 MPH and time (with an accurate timer), how long it actually takes to drive a known mile. The expressway mile markers can be used.
Of course if you can find out how by how many teeth the OSS ring gear has changed, that would give the percentage as well.
Once you know the percentage the speedo is off, adjust the rear-end ratio by that amount. That will become the new ratio reported to the PCM.
You may have to consider having a custom tune done or buying your own SCT programmer. Note, I would not solve this problem with a Speedcal. For the cost of the Speedcal, you could almost buy an SCT. The SCT will provide valuable ODB2 information for years to follow.