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My old diesel pickup does that, noisy input bearings (normal in GM manual transmissions) rattle with the clutch out in neutral. The throw-out bearing in my MR2 (which has taken me off the road) does the opposite, the noise starts when the clutch is depressed and goes away when the clutch is all the way out.
Wear in the input bearing/shaft is not unusual for C50 transmissions, it's the same design issue that causes 5th gear pop out. It will probably do ok in this condition for many moons.
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