Brain,
I think what you are looking for is...
THE INPUT SHAFT.
This is the shaft that comes OUT of the trans, and plugs INTO the clutch assembly. It's long, about 4 inches if I remember correctly. About 1.5 inches goes INTO the clutch. So you have to create a gap about that wide.
It's been a month of so since we swapped my trans, so I don't remember exactly, but if you've removed the starter, and all the necessary bolts, then the only thing that would prevent the engine from going up, is that shaft.
Good luck dude.
Elton