If you were planning on tearing it down and inspecting/replacing transmission components anyway, why did you bother starting a thread?
Seems like the tear down would answer your questions right then and there instead of us trying to speculate about what it could be.
If there was metal in there when you took it apart and did nothing more than cleaned some bearings, then you put another 600 hours on it...the question should not be "what's wrong with it" but rather "is there going to be anything in there worth using again".
Furthermore, 600-700hrs is a LOT of riding...top ends rarely last more than 100hrs.
Have you gone through 6-7 overhauls?