Why is my transmission 'clunky'?
If your vehicular experience is limited to automobiles, you may wonder why the gearbox on your bike will click and clunk sometimes when you shift gears. Is something wrong? Is my technique bad? The short answer is: No. The 250 has a type of gearbox where some of that is inherent and normal.
A normal forum comment on this issue is: "Congratulations, you bought a Kawasaki", but you should just accept that "that's just how they make 'em". There are certain elements of gearbox design that contribute to this phenomena, and the advantages outweigh the clunks.
Many newer riders may not realize that motorcycle gearboxes are a 'whole other animal' compared to the familiar synchromesh manual gearboxes in cars. There is very little connection between the two types.
Today's bike gearbox grew out of the virtually identical ones used by the English motorbike makers in the 1930s. Those only had four gears, with the clutch and output shaft usually on the same side, rather than clutch on the right and output on the left. But the principles were the same.
The Ninja 250, and most other motorcycles, has a sequential transmission. This means that you have to shift from one gear to the next. You can't skip, say, second like you can in a car. Your bike's transmission is also non-synchromesh, which saves weight and space, increases reliability, and allows for quicker shifts than the typical automobile transmission.
How shifting happens
With our 250 boxes, when you operate your shift pedal you turn a cam drum, which moves shifting forks sideways. It makes 'dogs' enter windows or slots in gears to lock gears and shafts together to get the various ratios you want. The resistance or clunk you feel and hear is the dogs knocking against the gears they enter, until they turn enough to enter the windows. Sometimes you hear no clunk and feel no resistance, and the dog goes right into the window, so you get an ideal shift. But this is a hit-or-miss deal, and you can't control it by your technique. The windows, by the way, are quite a bit longer than the dogs, to give you a better chance of hitting them, and also a quicker shift.
Why this design?
All this makes a more inexpensive gearbox to manufacture than a synchromesh box, plus it gives you the benefit of quicker shifting. In fact, what you have here is a gearbox that would have been regarded as a racing-quality box by the Brits of yore. The long windows give plenty of time for the dogs to enter(this is known as 'backlash' traditionally) so you can make a lightning-quick shift. The downside of the large amount of backlash is that you have a lot of slop and play in your drivetrain, which in fact we do. But this is inconsequential.
This form of gearbox and gear-changing is only possible because the gearbox parts are geared down a lot, turning only 1/2 or 1/3 the speed of the crankshaft. If such gearboxes run at engine speed, like the BMW Twins traditionally did, there is VERY clunky gearchange. Car gearboxes run at crankshaft speed, hence they need synchromesh to get a 'sweet' gearchange.
So, don't let that little bit of clunkiness put you off. It's a by-product of the quick shifting you get from your motorcycle, and it isn't hurting anything.