Ditto. From the tranny back in order, you should have the bearing with an open side facing the tranny for lubrication, then a shaft seal to hold the gear oil in the tranny. Make sure the seal is pointing the right way. The side with the spring should be facing toward the transmission. The side with the seal number printed on it should face the t-case. If it is a double lip seal then it doesn't matter.
Not sure about the flat towing problem. I can't recall what all spins inside the case when you go to neutral. I believe the problem in flat towing would be the bearing in the output housing of the t-case, not the bearing in the tranny/
transfer case adapter.