Poor Champ; I'm so sorry. A few years ago Jessie had symptoms which resembled Pemphigus; fortunately, it turned out to be a severe allergic reaction called a furunculosis. At the time, I learned there are different forms of Pemphigus and some are easier to treat than others. Did the vets tell you which form Champ has? Here's some websites with good information about the disease;
http://www.upei.ca/~cidd/Diseases/immune%20disorders/pemphigus.htm
http://www.vetinfo4dogs.com/dpemph.html
Did you see a veterinary dermatologist at U.T.; they may be more helpful in controlling the skin infections than a regular vet. I know Callie would recommend milk thistle to help protect Champ's liver from the side effects of the Atopica. Jessie has numerous allergies and there are a few things I have found helpful in preventing ear infections. Cleaning the ears regularly is very helpful; I use Epi-Otic;
http://www.virbacvet.com/virbac_dermatology/product/epi_otic_ear_cleanser/
A study I read on PubMed showed that this ear cleaner used twice a day cured bacterial and yeast ear infections in dogs in about 68% of the cases;
http://www.ncbi.nlm.nih.gov/pubmed/16598680?ordinalpos=7&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum
There is a product my vet recommends for dogs that constantly get ear infections. it's called MAXI/GUARD® Zn
4.5 Otic;
http://www.addisonlabs.com/ZN45Otic.htm
It is not an ear cleaner and can be used daily. I haven't needed it for Jessie but my vet says it's effective.
I wish I could help more but I will keep Champ in my prayers.
Life isn't about waiting through the storm; it's about learning to dance in the rain.
Janice