I recently went through this too while replacing my clutch. It sounds like the splines on the input shaft aren't mating up with the clutch disc. Easy fix, with the trans inserted as you had it, have one of your buddies turn the crank pulley (27mm) while pushing the trans forward. The gear will meet up and it will slide the rest of the way in. You could also rotate the trans to try to line up the gear, but thats a lot harder considering there isn't much room under there.
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