Aw, gosh - I really feel for you

- it's SO frustrating. One thing...you mentioned yeast...is there an odor to her at all? If so (or, even if not), then I'd say do a skin scraping for sure so they can see if yeast grows out in the culture. I think scrapings are about $25.
As for the protein - yorkies can eat high protein. The times they cannot is if they have liver/kidney/pancreas disease. Otherwise, grain free can do wonders for some. I feed Natures Variety Raw - and that might be something to consider. Keep in mind vets receive about 1.5 hours of nutrition education in school...so you may already know more than he does

.
Another thing you might try is "Relief Spray" -->
Relief Spray - 6 oz. _or_
Oatmeal Conditioning Spray:
Oatmeal Conditioning Spray, 17 oz - Jeffers
Here is a general article about atopy:
Allergy and Atopy Treatment in Dogs
Great link to learn about Omegas:
Omega Fatty Acids: Sources, Effects, and Therapeutic Usesin Dogs
I hope she gets better

. So frustrating. If you need a non-flax Omega, let me know and I'll hunt my link for that too.