That massage you're doing seems like it couldn't hurt. Hopefully it helps!
You are probably already aware of things like colloidal silver and oregano oil to bring take down the infection?
The FODMAPS elimination diets are useful for finding food allergies. You restrict basically everything that can cause issues in humans (there's a big list), and then slowly add things back in, and identify the ones that cause problems. It takes a while and isn't super fun, but it's natural, it's safe, and it can work.
I don't know if vomiting is a normal part of ear infection. Not sure what to make of that. Maybe a reaction to the suppository meds? Could be unrelated, kids throw up sometimes. Hmm.
Wish I could help more. Sounds like you're doing your best to treat the symptoms, while also looking to find and treat the cause. You're a good daddy!