My two cents;
I use Simple Green to scrub my hones with. A bio safe, great cleaner & degrease. if the hone is in really bad shape, I use EZ Off Heavy duty oven cleaner for 20 minutes, then scrub with Simple Green.
If you feel a raised blemish, I would pencil grid it, then gradually lap it until the blemish is gone.
But, I'm new with hones and I'm sure the guys will be along soon with more ideas.