It's probable that the combination of the gas and oil being left in the crank case are the culprit. No doubt the ethanol in our gas was a contributing factor.
I doubt the cases themselves have powdercoating on their interior surfaces, but Yamaha gets pretty sloppy with the side covers. If I'm right you could remove only thje side covers, fully eliminate any remaining paint from their interiors, flush the crankcase thouroughly, then refill and do a couple of oil changes back-to-back.
Definitely a new one on me. Does what you're seeing inside the cases appear to be softened powdercoating? Check your clutch before doing anything else. The binder in the clutches breaks down with prolonged gas exposure as well.