Need more info.
First off, try to eliminate the clutch, does the noise change when you engage clutch?
Go to motor.
Easy to do, look in the exhaust port. Do you see scratches etc.
Take the top end off.
If anything is amiss you'll see it, for all you know you might have a c clip thats wedged against the side of the piston riding up and down for the ride. Believe it or not engines can continue to run okay with pretty bad damage, it just takes awhile then it gets bad.
There are so many things this could be I would definitely take the top end off.
If you have not done this it is not as hard as it seems. Start with a clean bike go slow, if you have problems email here and anyone of several guys will get you through.
1) check piston, wear
2) check connecting rod bearings.
3 ) check lower end bearings.
4) check KPS, make sure everything moves smoothly, clean while your in there.
5) check cylinder for obvious wear.
If you do not have the tools bring piston+ cyclinder in to a shop to measure clearances.
If everything in the top end is fine I would then move to the water pump bearings . It is hard to diagnos with out hearing the noise.
What oil and ratio do you use???
The noise is not normal, all the above procedures should be in the archives.
Good luck