125-200cc Rattle/vibration

My 04 CR-125 has a rattle and vibration at idle, only
does it when the clutch is out if you pull it in it goes away. I thought it was a bearing on the main shaft.
I removed the clutch and turned the main shaft by hand can feel the gears but feel no roughness or play in the bearings also checked the primary drive gear nut and fly wheel nut, didn't feel any play at the ends of the crank. the kick start idler gear and bearing feel good. the clutch basket and plates all look good. Does the pressure plate have a specific alignment on the inner hub, or does anyone have any other ideas, the bike shifts very smooth and runs good. but the vibration has me concerned, we just got the bike so
I have know idea how long its been doing it.