Hypothyroidism is an auto-immune disorder. I personally feel my Chewey had it because of over-vaccination. At the time, I didn't know any better and would get every vaccine the vet recommended -- sometimes even ahead of time, because they would make you fear that if you went over, then your dog was at severe risk. Also, before it was determined it was her thyroid causing the hair loss and sores on her skin, her vet gave her steroids and even injections when the sores would come back -- her skin would get these little sores that were raw, and she would flinch when I touched her. I thought it was odd that I had to keep going back to the vet for injections, so I tried another vet. She gave her antihistamines. They helped more than the steroids with the sores, but she still had the hair loss. FINALLY it was figured out that she had hypothyroidism. Once her thyroid levels were normalized, her hair started to grow back (came in a different color and texture than the rest), the sores went away, and she lost a lot of weight (she was overweight to start out with, even though I kept cutting back her food to help her lose weight before). She later had diabetes and Cushings Disease (another auto-immune disorder). When I researched the Cushings, I learned that her vaccines should have been stopped immediately when the hypothyroidism was discovered. If you still get vaccines, talk to your vet about stopping them. You can even get away without rabies. The label says to give it only if the dog's health allows it. If your vet will do it, you can have them right a letter stating that the dog is not healthy enough for the rabies vaccine. I believe most states will accept that.
Will the surgerry on Missy's eye take care of the swelling? Hopefully so, and then you will be able to stop the steroids.
As for the food, just research the higher quality foods and just try different ones. Every dog will react differently. I made Chewey's food for her, but that was needed because of her diabetes and Cushings disease. She got protein, vegetables, and cottage cheese. I definitely had to supplement her food with vitamins, minerals, enzymes, etc. Haley, my dog now gets mostly the frozen raw food mixed with veggies and cottage cheese. Sometimes she gets regular food. The closest thing to carbs that she gets would be starchy vegetables (lima beans, yams, etc.).