The input shaft difference is between 94 and up (v6/v8 the same) vs 93 and older. Ford moved the shifter location in the cabin and needed trans moved back a little bit. Hence longer input shaft.
As mentioned above, flywheel tooth count is different between 3.8 and 5.0, thus different bellhousing. I do believe they will bolt up, but some things (like starter) won't line up right.