Drop the pH. If your pool is vinyl don't go below 7.2. If it is plaster or filberglass drop it to about 7.0 and then filter for 24 hours to see if the stains get lighter or disappear. You might also want to test the darkest stains with a vitimin C to see if they lighten. If they do then another dose of ascorbic acid will help. IF they don't post back and we can try some other things.