My Boxer was allergic to most proteins, so we had to switch to duck or fish. The signs were a lot of mucous in the stools, no itching though. He also had lymphoplasmacytic gastritis which caused excess acid which would make him vomit yellow bile in the morning. If the acid was bad he'd have a dry cough because of the reflux. The problem was solved with the Internist prescribing Pepcid, giving Sulcrafate when he was on an antibiotic, and feeding him several times a day. A single carb, and single protein with low fat solved the problem. It also helped if I wrote down what was going on throughout the day. If his stomach was irritated he'd bring up all his food shortly after eating.
I don't think that's what you're dealing with, but it is not something that can't be managed if it's a food allergy. I think soy and flaxseed sometimes can be an allergy problem. Stress would also seem to be a factor. A three hour car ride would bring on an upset stomach, and he loved the car.
Hope things go well, no Boxer should have a bellyache.