Oh owie! Poor baby! Poor you!
First...have you had TBD testing done?
Second, I would compare the ingredients that you were feeding when you did the home cooked diet vs the Eagle Pack?
"worst bacterial infection the lab has ever seen possibly caused by allergic dermatitis" is what the pictures look like, and allergic dermatitis is usually a contact type allergy.
What kind of bowls are you using for feeding? If you aren't using stainless steel, I would recomend several sets of dishes so that you can sterilize them after and keep the bacteria or if it is a fungus from being reintroduced to his poor face.
Have you and your new vet discussed allergy testing? Constant allergic reactions can weaken the immune system opening it up to reoccuring infections.
Allergy testing isn't hugely accurate from what I understand in the food department, but I found it to be a good place to start with my allergy hound, and it was pretty right on actually for his food allergies. With is food allergies though, he was constantly scratching, gnawing, licking, and face rubbing.