Looking at your ball & trunnion driveshaft coupling face I am wondering if there were two different ones...one for auto & one for manual? The below photo is of my current piece that was on the trans that Keith Long built for my 64 Sport Fury 426 console auto. You can clearly see the matching indentation for your ball & trunnion face.
This is the same companion flange that is on my 4 speed transmission, the one with the recesses. The picture didn't come through with the reply. You go me to thinking and I went out to check.