Greetings, and welcome
My 2¢ on rebuilding the engine is don't waste your time and money. These are cheap, enough to get another used one, and keep riding. These engines are disposable, cheap and plentifully.
There will always be some sediments in the oil, I'd say replace the CCT, and see if that eliminates the Cam chain noise.
And how bjgh are you revving it? And how long? These engines are pretty tough, assuming you keep the oil up to level, clean, filter, and oil pump screen, etc.... Same to be said about the clutch.
These engines are known to make a knocking sound, which is most likely the clutch basket, which is nothing to worry about.
Read this
https://faq.ninja250.org/wiki/What%2..._the_clutch%3F
Hope this helps you out.
P. S. How many miles on it?