My advice (I'm not an MD) is that you get yourself to a medical practitioner (GI guy, naturopathic, whoever!!!) who takes deranged gut flora seriously. And do it immediately! Get that stool testing done, get rid of that yeast, rebuild the gut flora, reintroduce GSH, use lecithin and choline, work with your dentist on the expander issue (can it wait a bit??), ask if the Prilosec is negating her gastric lipase action . . . . do everything you can think of, and then keep doing it for 4-6 months. That is the usual time frame for turning around messed-up gut flora.
Ah, you poor things. I'm so sorry to hear about your struggles and frustration with this . . .