difference between '96 and '97-'01 NP231?

I've never read anything about any differences, since they went to the longer output shaft in '96, but the car-part interchange doesn't cross reference the '96 with the 97 up.

The input gear should be the same, and the output shaft should be the same, so the only thing I can figure is maybe the extension cover and/or the speedo sensor changed. Anyone know for sure?

No differences that I know of. The only reason I can think of that the list you're looking at has a split between 96 and 97-01 might be some weird parts interchange that also includes the 97+ TJ...