Wrong 01 Gt Computer ?

Seems more likely to me that the problem is in transmission. Perhaps a transmission from the wrong model year.

Perhaps a transmission with a VSS sensor was used in an application that requires an OSS sensor.

Here's some information that may help you understand the difference between a VSS and OSS sensor and why you just can't "swap" them.

T-45 Tail Shaft Swap
http://www.allfordmustangs.com/forums/4-6l-tech/140694-t-45-tail-shaft-swap.html

More information regarding the differences between a OSS and VSS sensor.

http://www.allfordmustangs.com/forums/4-6l-talk/1053722-1999-tranny-swap-into-1996-a.html

Well if this is an automatic PCM mated to a manual transmission I can see how that can cause problems.

Even with an OSS sensor there are differences in the number of OSS teeth between model years and automatic vs manual. And yes it is very possible there are a different number of OSS teeth between manual and automatic even in the same year.

IF the problem is just the number of OSS teeth is different that what the PCM is expecting this can be handled via a PCM re-programming very much the same as a rear end ratio change.