My 6th gear has been a little noisy in 6th gear, especially under lower revs. What's the most likely cause?
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Why do things simply when you can complicate them

Never really see any problems with NSR gear boxes so if youre sure it not a hooked front sprocket or worn chain the only thing that can happen is the output bearing can start to spin in the crank case. This causes some funny noises.

Apart from that pop the box out and have a look. Wet clutch boxes are pretty cheap to pick up or rebuild yours.
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If I have to take the carbs off once more...