
Reading the manual again and again is essential for the home mechanic to correctly diagnose a fault, quick fixes, especially sourced over the inter web, are mostly money pits involving the willy nilly replacement of perfectly serviceable parts. If you’re allowed spanners and you haven't already, you may want to
download the Honda Workshop and Owners Manuals here.
First gear clunk is normal and is caused by the stationary dog gear engaging with the rotating first gear. Clunking during 2nd and 3rd gear changes indicates a fault which is most probably to do with the drive chain or clutch but could be caused by other failures, start easy and prove where the fault lies.
Check the drive chain for adjustment, lubrication and wear. Is the the drive chain in a good and serviceable condition? Some reading of possible interest
here and
here Check the clutch operation - Warm the engine to normal operating temperature, then with the ignition switched off engage 2nd or 3rd gear and keeping the clutch pulled in push motorcycle forward. If there is any resistance or the engine tries to crank the problem is clutch slip where the clutch is not fully disengaging and could be caused by old or contaminated clutch fluid, old or contaminated engine oil, sticky or worn clutch plates or incorrect specification of engine oil. Another indication of clutch slip is when riding up a gradient in too high a gear and the RPM's increase but the road speed remains constant.
Other causes of clunking when changing into 2nd and 3rd gears could be due to worn or damaged gearbox internals such as selector forks, gear change ratchet mechanism, gear shift drum or gear dogs. All of which is most probably beyond the experience level of the average home mechanic or unqualified mechanic.