As long as you put enough sequestering agent in the water, and bring your ph down to 7 - 7.2, you should not get any more staining out of the water. It is important to put in enough sequesterant - more than what it says on the bottle, according to the amount of water in the pool. I think just by using enough sequesterant and lowering the ph, it should take the stains away, since there isn't any on the vinyl liner. After you see the stains lighten, I would take the chlorine up to shock, very slowly, about 2 ppms at a time. The chlorine should help break the "stuff" down, so it can filter out. You can also put a trichlor puck in the skimmer basket if you have a sand or DE filter. Another good idea is to get a skimmer sock, or cut the leg off pantyhose or tights - put the foot in the basket and leg around the basket. It will help to catch the really fine sediment. Hope this helps, keep us informed.