I can see some brownish stains, were you be able to remove all of that?
I will try a normal stain removal 9-9.5ph first on a small 1 inch area and see if that moves it or not. Then I will continue according.Don't go crazy bouncing your ph. Vinegar is an acid but I agree with the rust and whatever contaminants were trapped in your lines. In other words try to get your ph back to an acceptable level. Acid will set some stains.