Check out the diagram you posted, the large driven gear of the clutch basket is held on by rivets inside which are plastic buffers that got hard, shrink & compress. When I bought my bike I was going to tear the engine down due to the big end knock. Then some research showed its the worn bushes, see here for full details.
http://faq.ninja250.org/wiki/What's_that_noise_coming_from_the_clutch%3F
On the pic link I posted, the gear has springs in it, which is how most other bikes clutches are. I've reviewed a load of videos on the net & no standard next gen has the knock, but most pre gen vids do.