Not so much shoes or sewage smell but I can relate to the (faint) rotten smell mention. On my end, I can typically smell it when I leave my apartment and come back in and it sort of fluctuates sometimes I notice it when I come in; other times the apartment smells normal. To my nose, it's kind of faint but who knows what others sense as I pretty much can't smell myself.
Regarding the snacks, maybe you're gluten sensitive? Try gluten free options of the snacks and see how you react. I know I get less reactions when I make a conscious effort to eat little or no gluten but the problem with GF products is that many of them are packed with Sugar which I believe may be a contributor to the odor problem, so watch out for that too.