OK HN,
Can't get 'em to mate? Not the end of the world.
As I see it, worst case scenario: you might have to lift it out and recheck a few things. Best case: shove it back on the tranny a little harder, and
bing; it goes together.
Did you by chance have one of these to center the Clutch Disc as you torqued down the Clutch to the Flywheel?
They really help in the mating step.
You mentioned some Shift Fork work. What exactly was done to it? The Throwout bearing replacement was a good idea.
You can do it.
Steve