The stator looks good - there doesn't appear to be any burnt coils. Check closely for any broken wires. Is that a groove on the outside of the rotor? Does it look like something is making contact with the rotor?
I hate when problems doesnt present as obvious - but that is the situation you are in. After it is all cleaned and reassembled, run through all of the tests again to see if any of the conditions changes (sometimes taking things apart and putting them back together helps). If the results are the same (i.e 2 85 volts legs and one 66 volt leg, and not achieving greater than 14 volts at the battery terminals) - then something has to change. I would start with a replacement r/r. First because it's the least expensive item; secondly it's easy to get to; and thirdly it is the only item that hasn't been fully diagnosed (because it can't be). If that doesn't resolve the issue, you'll have to replace the stator. I would use an OEM stator - it's a known quality. Alternatively you could contact Rick's Motorsports in the USA. They don't have an FZ6 stator that they stock (because they don't fail) but Rick is able to do custom winds. It's high quality workmanship, but in the end it may not save you any money due to shipping.