Ask around your area, I'm there is a vet somewhere in CA that works with Koi. Might be far away and not cheap but if the koi is a large favorite one, it might be worth it. Kind of seems like, and is in a spot that often gets scrapes that than can allow fungus or disease to take hold.
A high concentration salt bath treatment might help at least keep in in check until you figure it out. Very hard to diagnosis via a forum.
Craig