When I read your post, seriously, I had to do a double take... pretty sure I wrote this exact post about a year and a half ago.
Here's our 'story'...
In late April (2011) I noticed Tillie had what looked like maybe a scratch. I thought perhaps one of the cats had gotten her or something. I trimmed around it and put neosporin on it. It healed up! yay! Then I noticed another one about a week later. There was no explanation and within 3 weeks, the backs of her ear flaps were crusted over with these weird scab things... she had them all over her chest and the top of her head. She never scratched any of them. Some people suggested it might be a flea allergy though, although no flea/s were ever found even though I was bathing her every few days at that point, in case... My (stupid) DH didn't want me to take her in, but of course I did. He thought it was something that would just 'go away' on it's own... So, I took her in, the vet did scrappings of the sores on her ear flaps to see if it was mange, mites or some other parasite. Nothing showed up. At this point he estimated she had well over 100 of these sores. So, his next step was to do blood work. His theory at the time was that it was allergies to what she was eating (Taste of the Wild Prairie formula). He said that her body was pushing out the 'toxins' much like a teenager does who has acne. The scabs were what he called "pustules". So he drew blood (a.lot. and Tillie is WHITE. they had to ask me to leave the room. lol) and sent it in for allergy testing.
The result? Massive food allergies. Tillie was discovered to be allergic to Chicken, duck, turkey, apples, carrots, berries, all fish except Salmon, oats, barley, eggs, and a few others I can't think of off the top of my head. Tillie was 9 months old.
So, the Dr actually gave her a prescription for something (do not remember what it was) that helped the sores heal up without getting infected and the allergy test results came back a week later. He was the one that started me homecooking with his recipie and then I went through Sabine who has been highly recommended many times here on the forum and she tweaked the recipie here and there and we found something that works long term for her. I have been home cooking for a year and a 1/2 now. I have 2 school age kids and a job, yet I make the time to do what is best for Tillie.
I COULD have chosen to keep her on a kibble that she WAS able to eat, but I figured it would be better for Tillie and actually cheaper in the long run to home cook. I DO have a bag of kibble she CAN have in the pantry and I give it to her about once a week for 1 meal, so just in case something ever happens and I am unable to cook for her, she will still be able to eat.
Hope my story gave you some hope and I hope the vet can help you figure out what is going on with your sweet baby and that he is on the mend SOON!