Sorry for what may be a silly question, but was this same transfer case previously bolted up to your transmission, and now will not reinstall, or is one or the other of the "halves" different or new, trans or transfer case?
Asking because if you've changed from an automatic to a manual transmission, the TC only uses (5) studs on the T4/T5, and all (6) studs on the automatic.
If the above doesn't apply, and the output/input splines really are aligned, there should be no reason for the TC to not seat correctly, unless there's some other physical/mechanical impedance. Just thinking out loud -- is the trans supported with a floorjack, like maybe sitting higher than it would be when supported by the crossmember? If so, could the transfer case be hitting the underside of the floorpan and binding up?
It's not terribly easy to do if installing the transfer case by yourself, but it does help to jiggle the TC output yoke back and forth (where the rear driveshaft bolts up) WHILE trying to push the TC onto the back of the trans. If there is misalignment with the splines, it should take just a fraction of a turn in either direction on the TC output yoke to get the correct alignment.
Hopefully this helps...
David