2 Stroke CR250 Clutch removal problem - flywheel stuck on shaft

That brand of crank is known for not being true right out of the box. I must also say that what you describe indicates a dirty bearing.

Paw Paw
 
If the crankshaft flywheels really are out of alignment enough to contact the cases you should be able to see it, and could darn sure tell with a dial indicator on the crank half for on either shaft where they are exposed.
 
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