Did you check if the curtain speeds still line up after the swap? The MX and Spotmatic have different top speeds and timing gears even if the physical dimensions look close. Curious what your 1/1000 and 1/500 shots look like, any banding or exposure drift across the frame? That spacer shim you pulled might have been setting the curtain tension or the brake timing, not just clearance. If it fires fine through a whole roll then maybe the tolerances really are that close, but I'd want to see a test roll before trusting it on anything important.

Been there with a shower floor that looked fine until you actually use it. Standing water is the worst, glad the laser level paid off for you.

A 6-point socket is not the same as an extractor, but it does grab better.