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Jnats are no miracle hones but used at the right moment in your progression the will do a good job. Using them is no rocket science and not more difficult than using any other hone IMHO. I like them...

Are you implying that the Naniwa 12K can be seen as the gold standard for Jnats?

If you find notches you should find out which stone caused them.
It could be the hone itself but could also be one of your slurry stones. Naguras too can have toxic inclusions and some lose some...