Can anyone give me some advice on my

Form experience, it's piston slap. The bike has a steel (boreable) liner that wears as the piston wears. Simple fix is to remove the cylinder and poiston and have it taken to the next oversize. Be sure that the establishment performing the bore job also cuts the exhaust port "eyebrows" back into the cylinder above the exhaust port. If the eyebrows are not cut in, the bike will lose significant RPM and will be very hard to start. Sometimes too much compression is a bad thing...

Since it's a '96, go ahead and replace the reeds. Fresh reeds will deliver slightly crisper throttle response.

does it change when clutch is engaged, my cr250 has hella clutch rattle and it was scary when i first bought it cause i though it was piston slap, but it wasnt.

This sounds pretty stupid but......I have a '90 CR500 with an aftermarket pipe. The CR500 pipe is so huge and has so many twists and turns that it very easily can vibrate against stuff. For the longest time I thought that I had some kind of an engine noise, but if I put my foot on the top of the pipe the noise it quits! The pipe looks like it has plenty of clearance, but there is so much pressure coming out of the cylinder it dances all around. Another stupid thing to check is your pipe springs, it they're on wrong or not tight, they make weird noises. Here's something to concider, if you leave a piston in one of these things too long, they tend to crack the piston skirt. You don't want to own one when the piston skirt breaks off!!! It's a scary thing buying a bike from a stranger, you don't know what that motor has been through. If in doubt, at least take the top end down.

'90 CR500....point, twist, hang on!