The history you give sounds like your guy has food sensitivities. I would suggest a couple of things:
1. Switch to a Limited ingredient food (LID) that only has one protein and one carb. Choose a novel protein your dog has never had (buffalo, lamb, bison). I like Nature's Variety Instinct but there are others.
2. If you can afford the expense I would do Dr. Dodds Nutriscan food sensitivity test.
NutriScan Food Sensitivity and Intolerance Test for Cats and Dogs
. It's about $300 but it gets good reviews. I myself am saving to afford it for my pup.
3. You can do an elimination diet on our own. Seems like you already started down that path. It does a bit of time to see results.
4. Make a 50/50 mix of water and Organic Apple cider vinegar. Wet a cotton make pad with the solution and gently wipe the inside the ear as deep as you can go without loosing the pad or hurting the ear. Do this 3 times a day. Be sure to dry the inside the ear after cleaning.
As for not agreeing with your vet. You wouldn't be the first, won't be the last. You could get a second opinion from another vet. Is there an holistic vet in your area?
Ultimately, it's up to you to use your best judgment.