I have an auto 98 xj, What input do I need on the t-case? 27? short , long?
Any info would help alot, I daily drive it and dont want to tear it apart till i could find out. Also what is stock wms to wms?

Research it. For your WMS measurement, go measure it, or once again, search.

I could do that but ... oh wait they're not stock axles. I could not find anything on here so thats why I asked

google works... why dont you use it? for stuff like that it is better to search google if you cant find it here.
http://www.novak-adapt.com/knowledge/np231.htm
stock wms is around 61 for the front 60 for the rear

Tape measures work well, too.

Since the other guys don't know the answer, the WMS distance stock is 60.5".

I don't understand what you need for the input shaft. What's your situation, what are you doing?