I have a T56 that I had the tail housing modded for a cable speedometer, I had it back together when I realized I forgot to put the magnets back in, I pulled the tail housing off and installed the magnets and I am trying to get the tail housing back on, but it won't go on the last 1/2 inch, I have the transmission inverted vertically with the end for the tail housing facing up and no matter what I do it won't go the last 1/2 inch, i cleaned the alignment pins so that's not the problem and I don't see anything wrong with tail housing or the inside of the transmission except the large c-clip holding a bearing race into the tail housing looks like it may have a little section the in not fully seated, I removed that cleaned out the area where it is installed and put the c-clip back in and it still has the overlap. I am baffled with this damn thing

 

The countershaft extension bearing race tends to drop down a bit. Spin and push it back up. Trans. assembly lube or a bit of Vaseline will help hold it.

Most likely is the 5-6-R shift rail assembly flops and gets in the way. It is supported at the ends, so until the extension housing is on, it falls to the side. Use a thin rod (screwdriver) tool to push inwards and laterally back and forth, and it will go into the hole in the extension housing.