OK.

16 x 30 pool? Maybe, 16 x 32? That's a more common liner pool dimension. But, I'm sure somewhere, somebody has made a 16 x 30 liner. Regardless: a 16 x 32 rectangular liner pool with a deep end typically runs 20,000 gallons, not 40,000.

Hayward S200 sand filter? And a Hayward chlorinator? Inline, or off line? The inline models are a TERRIBLE flow restrictor.

Dark brown stains at the water line often involve liner deterioration, sometimes because people have used acidic pool cleaners! But sometimes they are just people goo (lotion, body oils, etc.) Try scrubbing a spot with a thick baking soda paste on a damp sponge. If that helps, then that's a safe-for-vinyl clean up method. If it doesn't help . . . you may be stuck.

Metal stains are not usually going to be at the water line.

Is your pump running yet? Have you begun dosing with dichlor, per my earlier instructions? Are there leaves and branches on the bottom of the pool? Sludge? Have you vacuumed the pool yet?

Anyhow, as soon as you get the K2006, test your pool water, and let us know what you've got.