I recently rebuilt my 96 kx 250 top end this video is from the first start up, I noticed this bottom end noise. I know I will have some noise (clutch basket was grooved so I knocked down the high spots) but this noise is still here when the clutch is pulled, I also ran it on low oil in the case because I was told it was filled, but it took another half quart, so I'm hoping it did no damage
when I let my KDX200 case oil get low it ruined the bearing at the far end of the clutch shaft. grabbing the clutch I could wiggle the shaft due to that blown bearing. could be the same thing happens in the KX cases.