We adopted a dog with lots of issues, and I work with kids with neurological issues that usually have a gut component, so I will chime in here. I know the thread is old, and hopefully your dog is better, but if not...
With our girl, it was grass and environmental allergies on top of systemic yeast, which no one would help me get rid of, so I had to go about it my own ways. This is what I did/do:
1) Have the thyroid checked
Dr. Jean Dodds is recommended, as she uses baselines for the breeds, not just a general guideline for dogs, like some others.
I don't like putting animals on any medications, but get her levels ok and get her healthy while you work on other issues and then wean off and retest later.
2) Food Grade DE
Used internally to "clean out" any unwanted pathogens and yeast.
To rebalance the gut, hit hard the first few weeks and taper off. This will help kill yeast and other things in the intestines.
You can switch to a BARF diet for a while and see what happens... Ours cleared up immensely, but she was allergic to chicken and beef and pork made her agressive. She ended up doing really well on quail and veggie scraps. I would just cut everything out, start with ONE thing and then see what happens.
I used Vetericyn for clearing up hot spots and other issues but have switched to a Dakin's Solution of sorts.
Hope that helps!!