James, the transfer case's input shaft diameter (spline count) and length varies by the type of transmission it is bolted to.
Your conversion from a manual transmission to the 32RH 3-speed automatic for your '97 TJ means your transfer case input shaft will be too short to seal the new automatic transmission's output shaft which means the new automatic transmission will leak ATF like a sieve. There is an easy fix for that which involves installing an extended output shaft seal into the new automatic transmission that will effectively seal it without any additional modification needed at the transfer case. Just seat it into the rear of the new automatic transmission before you install it and life will be good. The old rear seal can be removed with a pair of pliers which is easily done.
The extended output shaft seal for your new automatic transmission is available from http://www.teraflex.biz/automatic-seal-extension.html