This touches on, and then completely ignores, one of the most probable areas of concern - additives. Emulsifiers that disrupt your intestinal lining, artificial dyes/flavors/sweeteners, fillers, consistency changers, and all the other tools in a food chemist's toolbox. Those should be individually investigated and problem ingredients eliminated (e.g brominated vegetable oil).

Also, fiber. The standard american diet is lacking fiber and protein.