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Good diligent diagnosis and good accompanying pics. This thread ought to be a good reference for others in the future.

An additional testing approach is to use the higher grit stones at a very different angle to the heavy scratches you're getting to be sure that the scratches are coming from the higher grit stones...

I recommend some more diagnostics with the stones. Do a few strokes on a 1-2cm lenth of stone and inspect. Then go to the next segment and repeat. See if there are zones with problematic grits. ...