Marie,
have you tested for metals? ( I KNOW it's a stupid question but I HAVE to ask!) What were the results? Sorry to say that much of the pool store testing results for metals are bogus. They just don't know what they are doing sometimes. Copper is pretty easy to test for but some of the other tests can be a bit tricky. You might want to get your fill water tested (assuming it's your house water) by calling up one of these water purification companies that do free water analysis and compare that to what the pool store is saying. Iron is fairly commen in well water in many parts of the country and is also pretty easy to remove from the fill water with proper treatment. From my understanding an ion exchange column is a cost effective solution. First thing is to find out what the metal is and try and figure out where it's coming from. Iron would not come from a heater but might come from galvainized pipes if it is not in your fill water.
BTW, what type of filter do you have and was it thoroughly cleand out after the "bacquaswamp"? I find it interesting that the stains appeared after the conversion from biguinide. The conversion process requires a high level of chlorine to oxidize the biguinide in the pool and that high oxidizer level is also a prime contributor to staining.

there might be no cure but if you have a workable solution I would stick with that each year. I would LOVE to find a surefire way to remove metals from poolwater that worked. I could patent it and retire!