Thank you for your response Goldfields, I appreciate your interest. As far as Cody being aggressive towards other dogs we have not seen that. The biggest change has been that he was scratching himself so bad that we put a cone on him to stop him.
Well we took him to the vet and had him checked out, the vet seemed to think that it was normal for the amount of hairloss to be occuring with the staph infection. She also said that sometimes the hairloss can occur 6-8 weeks after a particulary stressful event in the dog's life as it takes that long for the hair to actually fall out. Makes sense considering he had the cyst removed and he absoulutly hates going to the vet. She also said full hair regrowth takes as long as 6 months. We went ahead and had his blood work done and that all came back ok. I asked her about the hypothyroidism and we had his blood sent out to have the thyroid levels screened.She didn't think that he had the symptoms of that, but just to make sure we had it screened. We won't hear back from that for 5-14 days. So barring any issues with the thyroid it seems that all we can do is wait. I'll post what we find out.