Maybe its not the gearbox but due to the clutch?
I found this after a long research on this rainy day here in Montreal...a lot of it makes perfect sense to me...
1) Most motorcycle clutches use multiple plates, which do not free completely (and separate fully from the adjacent plate) because they are contained in an oil bath (the gearbox or engine/gearbox oil).
Consequently there will still be some spinning of the input shaft when the gear selectors select whichever gear is there.
Even dry clutches still do not completely free when pulled in, and you might have to wait for 10 or 20 seconds for the input shaft to slow or stop, before being able to make a noise-free selection.
You could also find, if you do that, that the gear will not actually engage because it has stopped at a point where the engagement "dog" cannot fit into its mating slot(s). That's a little bit like what happens (except in reverse) when you hold the clutch in too long while coasting to a stop, or stop in gear and are unable to select neutral.
The "clunk" is not a sign of a problem, nor is it a problem in itself.
Then changing from 1st to 2nd is also a little rough, but then each gear upwards is fine...
Whats the mechanical reason for this? and is it present in all bikes?
The difference in gear speeds between 1st and 2nd is usually greater at the bottom end of the gearbox, hence there can be more noise because the sliding "dog" has to mesh with another "dog" spinning at a different speed..
However, a skilled rider will compensate for this by preloading the gearchange lever slightly and experimenting until he (or she) finds the correct "speed of lever operation" to make a clean, noise-free change. It's possible.
But once again, this is not really a problem.
Most bikes have this issue, but most good riders learn to change to minimise it. It makes you look better...or sound better. ;-)
The higher the gear the less difference in speed between components, so that there is less tendency to clunk. However, if you delay the change by holding in the clutch for a few seconds, you should be able to get quite a good clunk. ;-)
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