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When I push my bike into the garage after riding I notice a loud clunking from the primary/trans area. I never knew what this was but I did have a small trans oil leak. So now that the engine is being rebuilt and I have it ripped apart, I've fixed the leaks (trans seals) and found the source of the clunking. if I hold the transmission mainshaft in one hand and rotate 5th gear with the other, I can get that clunking. It sort of feels like a really bad gear backlash. Other than this clunking, the transmission works fine.
I suspect that 'backlash' may be the drive dogs, rather than the gear-teeth themselves. It would be worth taking the top cover off, to study more closely what seems to be going on. I had a similar problem years ago with a BMW flat twin. It was cheaper to 'fix' that by buying a secondhand transmission.
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