Two things first -- Welcome to Yorkie Talk and I am so very sorry that Rusty has this mystery illness.
I would start with his food..... change it -- sometimes food manufacturers change the formula and/or sometimes these little guys can develop allergies to certain ingredients. It might be a good thing to "home cook" very bland food for him for a while and then start adding back other items and his dry kibble and see where that takes you.
Good luck and sending many hugs
You will probably get prayers (mine) and good luck wishes because this site is full of very caring prayerfull people.