not read all ya posts mate so not sure if you have actually sorted this or not . . . .
I put and engine is a cossie recently and found that if you put a little scissor jack under the box to raise it slightly, leave the box in gear and spin the flywheel with a leaver bar (whilst wiggling the box in) it will slide right in. . . . .asumming clutch is properly lined up . . .this can easily done by eye though mate
Goodd luck