Worst case would be that the input gear is either too long or too short (manual inputs were consistent, but there were two or three lengths for the automatic inputs,) and both 'cases on the same side of the split for the input gear helix angle, so it's a simple swap. May as well change the input bearing and seal while you're about it.
Of course, if the input "stick-out" is the same length on both 'cases, don't even worry about it - just throw the replacement in and you're good.
Either way, change the output seal on the transmission, since you're there anyhow. And, I'd change the input & rear output seal on the transfer case, since you have the opportunity (the front output seal is difficult, but you can change that one once you've got the 'case in. The yoke nut is torqued to something like 200 pound-feet...)