Ds2 had milk /soy protein intolerance as an infant (he out grew it). I was breastfeeding and cut out all soy from my diet but after seeing a dietician learned I could eat soy fats, ie. soy lecithin. Not sure it would work for your ds. The dietician we saw specialized in pediatric allergies and had tons of info for me about shopping and reading labels. Our insurance covered the visit but her fee was really reasonable.
There were 2 brands of 100% whole wheat bread that were completely soy free. I'll look next time I'm at the store.