Yeast Problem?

At the end of July, my sheltie, Henry, got skunked. We bathed him several times with Nature's Miracle for skunk smell and since we had to bathe him so much, he's been very itchy, flaky, and patchy all over his body. At first I thought he was having allergy issues, but I read that yeast can become a problem especially with over-bathing (and the symptoms of yeast overgrowth that I read about were consistent with what was going on with him). I have done a lot to try to get rid of the problem including anti-fungal sprays and shampoos, fish oil, etc. I haven't taken him to the vet yet because I read that vets typically give similar shampoos for such problems. I'm starting to worry, as he still has these giant flakes and now I can see through his coat to his skin, and his coat was so thick and beautiful! Has anyone dealt with something similar? Any thoughts on what to do/give him? I want him to get relief and I don't want him to lose his coat! I also wonder if the hair loss has to do with him shedding/blowing coat/the time of year. Advice appreciated on how to get rid of the problem and how to help the hair grow back. Thanks!