A thinner washer behind the inner clutch hub should allow you to tighten everything down, and they should spin freely without ANY plates installed, just tighten it up and see if they can both spin.
This can be an issue as small as .005 (5 thousandths), but you should be able to lock it down, and they should spin independently.
It's easy to check anyhow, just report back here and hopefully we can get you figured out...
I am not familiar with that particular design, IF a mainshaft had an extra or incorrect washer in it between the two ends of the shaft, that would create the same issue as it sucks in that mainshaft too far.
I know you were careful, but silly things screw us up all the time, lots of silly things! Hopefully your trans is back together correctly; But, it would probably shift great with an extra washer or a misplaced washer in the tranny,but it could be wrong.
Most mainshafts seem to have 1 to 2 mm's of side play/thrust when the cases are locked down.
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