Thanks for the detailed reply, PoolDoc.
I shocked my pool (twice) and added agaecide (non copper based) prior to your reply, at the recommendation of my pool installer and as I had little to no chlorine for 8 days. Luckily the brown stains have not reappeared on the pool liner (that I can see anyway) but the pool is still a green/teal and not fully translucent.
We are using Sta-Rite 20um filters, I think they are DE but I'm not sure. I just bought two brand new ones last week as I wondered if that may be the issue. The water is the same water from last year and we had ZERO problems... I guess we were lucky as it was a our first year. I have no idea where the metals came from... we had a few leaves in the pool at closing/opening and we had a new heater installed in Mid May at the time of pool opening. When the water is tested at our pool installer they do not register significant metal levels.
At this point I am ready to have the water switched out. I spent $4000 on a new heater, $1000 on opeing and stain remediation and the pool has been open a month with not a single swim. I just want the pool useable and if a water switch out is the only way to do so then so be it. Thanks for your help and let me know if this additional information sparks another thought for you.