Do you have your GSD on a flea and tick preventative? Just because you have not seen any, does not mean that the dog does not have any. Sometimes, in a very sensitive dog, it only takes one bite to start a horrid reaction that just perpetuates itself with more scratching and itching.
My senior male GSD (rescued from a life on a chain) was very itchy after I pulled him as a foster and then adopted him. His allergies, however, were environmental rather than food-based. My vet put him on Hydroxyzine (a prescription antihistamine) and he stopped scratching within hours), We did a very short course of Prednisone (steroid) to stop the itching and then just continued with the antihistamine. It has worked wonders for him.
Sabra - female GSD - born April 30, 2012
Sargeant - rescued senior GSD male/foster failure - approximately ten years old (August 2013)
Max - rescued GSD - Dec 22, 2010 to March 7, 2012 - at the bridge
Sable - rescued GSD - at the bridge