Hi John, welcome to the forum!
We did a similar conversion on an SSie and when we fitted an old speedo from the Superbike range it still didn't read correctly - mainly noticed in the speed reading rather than the mileometer.
It turned out that the speedos were different even though they look identical and the drive cable fits! We changed the speedo drive (that goes on the axle and connects to the other end of the cable) to a Superbike one and it started working, so must have has a different drive ratio to the original.
I had a look at the part numbers but it seems that the earlier Supersports may have had a different part numbers to later ones - maybe this is where the difference is?
2000-01 SSie
Speedometer (GB-MPH) 401.4.012.1A
Speedometer Transmission 8000.74049 (this pn doesn't look right to me!)
2002+ SSie
Speedometer (GB-MPH) 401.4.018.1A
Speedometer Transmission 498.1.009.1A
2002 Superbike (748/998)
Speedometer (GB-MPH) 401.4.032.1A
Speedometer Transmission 498.1.009.1A
You can find the part manuals online:
http://ducati.com/services/maintenance/index.do It will be worth trying to figure out which speedo it was swapped to and then you can figure out if you need a different drive to match it.
Hope this helps!