Widespread Rust

Thanks in advance for any guidance. I have a 26 guage painted steel, standing seam. roof on a 6 pitch installed in 2004 from roll stock. It's my home and I was the general contractor. A metal roofing contractor did the install. A chimney leak (failed flashing caulk) got us up on the very tall roof last week. It's a simple A without valleys etc - like a barn. There is widespread rusting throughout the roof. Mostly nickel or dollar sized spots but also some irregular spots and some areas as big as a dollar bill folded in half. No denting.Every run is affected - probably a spot every 4 feet in each run. I have the original proposal. I have payment checks. The installer is still in town. I have the original color chart and an actual piece of the roof from the install. I won't mention the manufacturer here. They are a reknowned company. Unfortunately the installer did not submit warrantee paperwork and has not kept records from 2004. Only our payments to him are in his computer system; they had not fully computerized so there probably are no receipts to show the purchase though we may be able to find supplier records. Obviously we still have some investigation to do. Here's my question: Generally speaking, if facts indicate clearly what roof is on the building, and if facts clearly indicate a material failure(in this case the paint),do manufacturers in this industry stand behind their products when warrantee paperwork does not exist? I am a masonry contractor and I work with warranteed materials. I believe that we are bound by that old idea that a product must be fit for the purpose for which it was intended, but I'm not sure how that might apply, or if it should apply, to a failing 9 year old roof. Any help would be appreciated to indicate how this industry generally handles warrantees in a case similar to this. Many thanks for your help.