If by chance you’re new to riding or never learned about proper shifting, then perhaps what you’re experiencing is in fact normal and possibly enhanced due to lazy or poorly timed shifts.
If by chance you’re pulling in the clutch lever
for a few seconds as you coast and then make your shift, it will make for a stiffer feeling shift lever
and more pronounced clunk. This clunk will always be more pronounced in the lower gears than with the higher gears.
Here’s what happens in simple terms. As the bike is moving, the rear wheel
is obviously turning, which in turn is driving the countershaft, but the main shaft that’s spun by the engine is now at idle speed or spinning at a much slower speed when you pull the clutch lever in. The longer you have the clutch lever pulled in, the slower your main shaft speed will be up to a point. Under acceleration the engine is turning the rear wheel, but under deceleration the rear wheel is turning against the engine. In both of these states, torque is being applied through the gearbox, which means there’s a load against the counter and main shafts, the gears, engagement dogs, the clutch, etc, and the amount of difficulty and clunking in shifting is related to the difference in speeds between these two shafts. The greater the differences, the more difficult your shifting will be and the more pronounced your clunk will be.
Now, the reason you’ll get a clunk when you shift from neutral to first or second gear while you’re stopped is because the speed of these two shafts are not in sync (counter shaft is stopped while the main shaft is spinning). The reason for a clunk while shifting into second from first gear while you’re moving is because the shaft speeds are again out of sync, but in this case the counter shaft is moving while main shaft is at idle or slowing down with the clutch lever pulled in. The larger the difference the speed is between these two shafts, the more difficult the shifting will be in addition to more wear & tear on your gearbox components whether you have the clutch pulled in or not. Even though the clutch helps to lighten & transition the load, it doesn’t completely eliminate it. Slow lazy poorly timed shifts can absolutely cause more pronounced clunking and or additional wear & tear on the gearbox components.
You want your shifts timed so that they occur when the engine speed closely matches the rear wheel speed (both shafts spinning at close to the same speeds / minimal loading between the components) and this allows the engagements dogs to mesh softer and smoother with the gears.
Proper shifting techniques are rarely taught and most people have no idea what truly goes on inside the gear box, including many people that work in motorcycle shops based on my experiences. Proper shifting involves good timing between your shifts and it’s a technique that takes practice to master. The idea behind good shifting is to time the shift so the counter & main shafts are spinning at close to the same speeds (minimal loading) as you make the shift and this allows easy shifting that’s not hard on the gearbox components.
When up shifting, you want to momentarily roll off the throttle as you squeeze the clutch lever so the bike isn’t speeding up or slowing down. Then promptly make a firm shift, let out the clutch lever as you’re rolling the throttle back on. With practice, it becomes a split second momentary reaction without giving another thought it and shifting will be as smooth as butter at lower to medium engine speeds, especially in the higher gears. When downshifting, you should follow the same procedure except that you’ll be giving the engine a little throttle (or a quick blip) right before you shift down and this will help speed up the engine (main shaft) so it more closely matches the wheel speed (counter shaft).
I hope I typed this clearly enough because I was rushing through it quickly so I can leave town in time for 4+ days of riding