Yikes!

This is a bullet you'd really better bite and have the whole thing
checked out. You should be working with a feeler gauge when checking
final clearances around the flanges. It should be rechecked after the
boat is launched just for hull flex.

Get it right now. It will never be easier or cheaper.

BTW there is a way you can check the shaft coupling in the boat but it
takes some rigging and doesn't tell you about other things that should
probably be checked with the kind of history you relate.

--

Roger Long