In my opinion this sounds exactly like a food allergy. I would keep weening him onto the new food and see how that goes. Look to see if your new food has any gluten and grain. I know you do not want either of those. Keep a CLOSE eye on him when totally switched to the new food and keep track on his behavior. Sometimes it takes up to 6 weeks to see improvement and to locate the allergy so dont worry.
I am going through the same thing with my older dog. He has developed an allergy and we are starting with his food. It is very important not to change too much all at once. That way you can weed out the possibilities of where it is coming from. Also... look into the treats you give him. I think people tend to overlook the treats.
Another suggestion is to try MinkSheen shampoo, I have not yet tried it but plan to! Look it up on here and read a little about it. I know Westbrook Dog sells it as well.
Good luck!! keep us updated
