OK.

I had to do some research.

It looks like the pump and filter may be from http://ecoaquapro.com/, and your 'sanitation system' is from http://mysimplesalt.com/, which looks like a re-branded and re-labeled version of "Permasalt" copper based system, discussed here http://www.poolforum.com/pf2/showthread.php/16701

Let's operate with the assumption that the pump and filter are OK. But the MySimpleSalt is NOT.

Stains can be a problem any time copper is involved. Fortunately, the shocking and floccing process you have ALREADY gone through has probably removed most, or even all of the copper.

Let me give you a list of steps to follow . . . and then some questions I need you to answer.

1. Keep your pump on LOW speed, running 24/7

2. Test your water, post the result, and TELL ME WHAT YOU USED TO TEST!

3. Add 1/4 gallon of 10% Walmart pool bleach in the evening any evening the chlorine is below 2 ppm

4. Take pictures of your pump, your pool, the simply salt system and the LABELS of the shipper product. I particularly need to see the EPA Est # listings. You can email them to poolforum@gmail.com, text them to (423) 300-6560, or use Imgur to post them in this thread (instructions: http://pool9.net/postpix/ )

5. Tell me if you are on a tight budget or not. The easiest and fastest way to clean up and get things running smoothly will require you to buy some stuff now (mostly from Amazon) . . . and save later. But if your budget is tight, you can put in some extra elbow grease, take a little more risk of stains and algae, and spend less now. For example, removing phosphates WILL make things easier . . . later. But it costs $$'s now.

6. Tell me what you know about your well water. Well water is often -- but not always -- a problem for pools. It depends on what's in the water. Do you have a softener or water treatment system? Is the pool filled via that system, or through a bypass? Does the well water have iron or manganese or sulfur in it?