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Hi ive had my 2006 kdx200 for a while now(2.5 years) and while riding with my dad on some dunes i encountered a knocking noise (loudest between gears 2-3 but can still be found in other gears) it's hard to describe it's like it's missing a tooth on the gears but Idk. I don't think its kips because it appears above idle and goes away at very high revs but you have to be in gear and driving.

This bike is really beginning to drive me crazy I feel like I'm fixing more than I am riding

(Just did top end)

Thanks Tomas

Any noise like that coming from the transmission should be a concern that gets addressed sooner than later. I would suggest first draining the oil and taking a look at it, then remove the right side engine cover and start inspecting. Likely you will have to split the cases if you don't see anything obvious though.

Don't know if this will tell you anything but I drained the oil and found a bit of metal fragments in it. Going to look at the engine cover now

Cheers Tomas

Well, that's not good. You say you just did the top end, I would inspect the bottom of your KIPS actuator to make sure the pin is still in place, gets broken a lot during top end jobs because folks don't realize its a LHT bolt at the top. But since you say it only happens when not in neutral I'd be ready to find some damaged transmission gears. You will have to split the cases to inspect them.