Something in the way? Not quite lined up properly? Pull it, make sure everything is clear. When it goes back on, make sure it is straight..

 

I will try that the morning. It is hooked to the trans. Just a gap

 

Not even worth it ! Parts will cost mor than buying a good used T-case !

 

Already rebuilt. Rockauto was $100 for kit. Just trying to get it reinstalled.

 

Not really. To replace it with another high mileage np231? Yeah. Rebuild kits are rather cheap and the cases are very easy to rebuild.

 

Took it back off no issues. Put it back up and it still wont go on. Same gap as before. Wiggle it and nothing....? Any thoughts?

 

Trans in neutral. I spin the shaft and the transfer case moves in eliptical motion. Any thoughts?

 

Dirt, or some other crap in the splines? You could try putting all the bolts in, and then try drawing the t-case in, by tightening them in the same kind of pattern you would use for lug-nuts. Don't reef on 'em though, might break something.... See if it is interested in pulling itself in.

 

Shaft runs in a bearing at the bottom of the case - if it's not all the way seated you'll have the gap you refer to, I think.
Dab some paint on the end of the input shaft and check to see if it is seating all the way into your tranny output.
If so, your problem is with reassembly.
Good luck. I just replaced the fork in mine for the 2nd time. Did you ever get it figured out?
Patrick