Off the top of my head - havn't really thought this through.
Old setup before teardown - pins no longer active, shaft free to move fore and aft, shaft moves forward, contacts bolt in back of transmission, noise generated.
Torn down, put back together without pins, shaft in roughly the right position. Ininial tests seem ok. Short drive with proper loads being transmitted. shaft slowly moves forward, contact remade with trans bolt, noise reappears.
I'm not saying that's definitely the problem, but it could be a possibility.
Mart.