Output shaft bent on a 904

Well for starters you can't check the tail-shaft in the vehicle the way it was with a dial indicator, that has to be removed put between to dead centers and checked over at different locations of the shaft and then if it does have a issue it needs be rechecked in a v blocks on the bearing surfaces and then gone to the same areas it showed up in the dead centers.
So id bet he never had a good shaft or a non competent shop or the bushing was just worn out.

It is very possible to have a new shaft and have a vibe especially if it was bought thru shipping, and or using old stuff laying around isn't the way to say you checked it, shafts laying around could easily be knocked out of balance by being dropped or whatever else happened to them.
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If you have a vibe for 17yrs you should have leaks also.