One think you'll want to be wary of is if you have the TC installed all the way on the transmission side. I had my transmission in and out a few times last year and in my experience the alignment was only difficult when I didn't have the TC installed all the way. There were 2 removals/installs where I didn't spin it around enough to hear the requisite clunks and ran into a bunch of issues.
The first time it behaved similar to what you may be experiencing now where it was in just enough to get clearance from the flywheel but not enough to engage the keys on the transmission pump. Fired it up after the reinstall and it was in permanent neutral. The second time I didn't even have it close and ended up bending the alignment boss on the torque converter and which I had to send out to get fixed. The FSM has a spec for TC distance from bell housing that you would think would cover this but at least the second time I checked that and it still worked out poorly for me.
The third time I spun the TC around a ton and ended up finding the extra axial clunk that would now be obvious to me if I ever did it again. Fingers crossed you got it all the way in and just have some alignment gremlins but if you weren't super anal about getting it spun around and clunked in it might not give you any drive.
The first time it behaved similar to what you may be experiencing now where it was in just enough to get clearance from the flywheel but not enough to engage the keys on the transmission pump. Fired it up after the reinstall and it was in permanent neutral. The second time I didn't even have it close and ended up bending the alignment boss on the torque converter and which I had to send out to get fixed. The FSM has a spec for TC distance from bell housing that you would think would cover this but at least the second time I checked that and it still worked out poorly for me.
The third time I spun the TC around a ton and ended up finding the extra axial clunk that would now be obvious to me if I ever did it again. Fingers crossed you got it all the way in and just have some alignment gremlins but if you weren't super anal about getting it spun around and clunked in it might not give you any drive.