Do you have a couple of pics first? If you got it to slide in that far, You've engauged the pilot bushing. From you description, I can't tell if you if you've got the drive shaft connect to the differential or you can,t get in far enough. Like I said above, a rebuild tranny will have a very tight bushing. Put a little 90 weight on the outside of the yoke and see if it will slide further in. Last question, how long is your yoke? I want to make sure it is not too long and hitting the speedo gear.I will try to align the tail housing tomorrow and see what happens.
Thanks