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I appear to be missing a gear in the box but not sure which, its either 3rd, 4th, 5th. Clutch is correctly adjusted, also the gear selector, the engine has had a complete rebuild and the trasmission looked fine on visual inspection. Any ideas?

Are you noticeing this "missing gear" while actually riding the bike ?

Ues, but having diagnosed the problem further it looks a bit more serious, can't select 6th and jumps from 5th to 3rd on down change.

Could just be something worn or faulty in the selector mechinism or something wrong with the gearbox itself like worn/knackered dogs on the gears