Oh wow, that can't be fun. A couple of members have had kitties with crusting or scabbing on the ears, but I don't remember the cause - it may have been a fungal infection.
I've never seen this kind of reaction from a food allergy, but I would definitely cut out those treats in case it has an ingredient that he's allergic to.
Is there anything else he could be allergic to? Did you start using a new household cleaning product or detergent, for example? Several years ago, my cat licked off the hair at the base of her tail. The vet thought it might be a food allergy, but it turned out that she was allergic to the carpet deodorizer that I had started using, a powder that you sprinkled onto the carpet then vacuumed up.