does it click more when you are turning with throttle?
that could point to the inside of the differential.
The other trans gears it is usually pretty easy to identify bad teeth. And you would usually eventually lose all drive if the outside of the diff, input or intermediate gear stripped.

you may have over tightened the trans case when putting it back together, which could be the cause of the binding you noticed after working on it. That can even happen on my SC10 diff.