It does sound like you need to get your cya down. This is what I would do first:

Drain and refill about a third of the water.
Add calcium to get it up to 250 - 300
Keep your ph at 7.2
add bleach to get your chlorine up to the best guess chart of chlorine and cya that is in the sticky in the chlorine forum.
Add the bleach slowly - one jug at a time
If you see stain start to come back, then add more sequestering agent.
If the stain persists more than a day after the sequestering agent, and your ph is still no higher than 7.4 add more ascorbic acid (or citric acid).
Keep the pump running 24/7.

I think after doing this the water should be fine - whenever you get high chlorine along with high ph and there are metals in the water and not enough sequestering agent the metals will fall out and stain the surface of the pool. If you have metals it is always a good idea to keep the ph around 7.2. I always use the sequestering agent first before any stain treatment because it will generally lift any new stains. Let me know if you have any other questions.