What needle clip position are you running at the moment ?
Its always advisable to run rich with raising the needle and not increasing the oil quantity. 4% is a good ratio for the running IN time. Increasing further the oil quantity will lean the mixture out as the proportion of oil goes more !
I would suggest move the clip to second position from bottom of the needle - for the complete running IN period. And them move it to centre after the running IN is complete.
Also set the airscrew proportionally.
For the gear shift concern - I presume that you have serviced your clutch assy and set the clutch push rod pin as per the service manual. I also presume that the clutch cable is been adjusted as per the manual free play settings.
If you have not then here is the go
- Set the clutch cable adjustments at the clutch lever as per the manual.
- Remove the generator side cover and loosen the lock nut. Screw the push rod untill it butts. Now loosen the push rod 1/4 turn out. Lock the lock nut.



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