I am assuming there is a difference in the length of input shaft sizes between the 93-97 model years and the 98-02 model years. Is this correct? Can anyone confirm this?

I presently have a rebuilt tranny with an overly long input shaft.

 

Sounds like you've got an LS1 T56. Inputs are definately longer of the LS1's. There's a lot of other dimensional differences too. Check out D&D performance for a chart showing differences.

Steve