1. hold a vitamin c tablet against the stain (which is underwater--this is important) for about 30 seconds. If ascorbic, citric, or oxalic acid is going to work this will tell you. If there is no change go to next step. If it works do an ascorbic acid treatment.
2. fill an old, white cotton sock with dry acid and tie the top. Fill a small Tupperware container with stones or rocks (we want it to sink and not float) and cover, rubber band the sock to the underside of the container and place on stain (which is under water). Let sit 45 minutes but check at 15 minute intervals. If stain lifts or changes it is not organic and is metal. Proceed to step 4 (sponge test)
3. Take a trichlor tablet, crush it up and put it in a white sock (NOT the one you had the acid in), affix it to the Tupperware container. Brush the stain to disturb any biofilm and place the sock on the stain. Let it sit for 30 minutes. brush well again. If there is any change to the stain it is organic. Organic stains often require quite a bit of scrubbing and an oxidizer to get them off of plastic surfaces. Think of it as a form of mildew (not completely true but there are similarities). You know how hard mildew stains are to remove and they are organic.
4. If step 2 worked the stains are metal and probably copper. The problem is removing them from plastic or fiberglass, which is not easy, since they cannot be acid washed like plaster. Get a bottle of HEDP based metal sequestrant such as Proteam Metal Magic and a cellulose sponge (such as you use to clean the kitchen or bathroom). you will also need your rock filled Tupperware container and rubber bands. Rubber band the sponge to the container and soak the sponge with the sequestrant. Place on the stain. Check in 5 minutes. If the stain lifts and the area under the sponge is back to it's normal color it's metal, go to step 5. If it doesn't resoak the sponge with sequestrant and place on the stain for 15 minutes. If it lifts go to step 5, If it doesn't resoak the sponge and let it sit for 30 minutes. If it lifts go to step 5. IF the area near the sponge turns yellowish at any of these times the stain is organic, go back to step 3 (or use the sodium percarbonate). You WILL need to scrub and use an oxidizer like sodium percarbonate or high chlorine levels (which can bleach a liner--percarbonate is a bit safer but it still can bleach. Think of it like a color safe powdered bleach compared to liquid chlorine bleach that you use in the laundry--it's not but the analogy holds.)
5. Make sure the water level is above the stain line!
If the stain lifted in 5 minutes add one qt. seqestrant per 10k gallons.
If the stain lifted in 15 minutes add two qts. seqestrant per 10k gallons.
If the stain lifted in 30 minutes add four qts. seqestrant per 10k gallons.
Don't try t get away with adding less. It won't work.
The pool will probably get very cloudy for a few days to a week, this is normal. Run the pump and filter 24/7 for about 3-4 days. Check the filter pressure and clean as needed. The pool will eventually clear on it's own. Just let it run it's course. Keep your chlorine levels normal and do not shock while treating and for a few weeks after. This should remove just about all the metal stains.
:grrrr: 
)We are a little concerned because we have a non-functioning heater that my husband "unplumbed" from the system once we realized that it was leaking. However, we don't know how long water was circulating through it before he got it disconnected, and when he found the leak, it was coming from a pipe that had corroded, so who knows what got pumped in...
