Jakebear, let me take one more stab at this before I call in the pros. Are these areas gritty, feels almost like sand? If so, you've calcified your pool (aka scale), and will need to adjust the pH and alk to alieviate the problem (though a look at your numbers scaling doesn't fit ).
You can use the ascorbic acid to test for metal stains without having to treat the whole pool - place a big ol' pinch in a stocking and rub at a small portion of the stain for a minute, if it lightens then the stain is metal. If that shows no results, try the same using some of the powdered shock, but let it sit for an hour (Trichlor pucks are also good for this) - this tests for organics. Finding out the type of stain is the first step in treating it.
While I'm at it, why do you keep the return 'eyeballs' so tight? They work just fine without being 'reefed in' and it's much easier to change the direction of them.