Hi John --
I have not had genetics and muscle testing. And, as you noted, celiac testing is notoriously unreliable...as are the serum tests for other food intolerances, I might add. I don't buy into the theory that skin will react the same as more direct influence in the gut in releasing antibodies. Those represent completely different hypersensitivity models. Also, the small intestine biopsies for celiac can be unreliable as well, since the disease doesn't always affect the entire intestine consistently. So, a biopsy site, or several, may actually return normal samples.
I took famotidine for about a year until I developed a tolerance for H2 blockers. At that point I tried several PPIs, but all produced crippling headaches. I've had to rely upon timing of meals, sleeping on an incline, and Gaviscon before bed. (Although, I stopped the Gaviscon about eight weeks ago.)
My asthma symptoms and shortness of breath have completely resolved. I had lived for so long with reduced lung function, I still marvel at how much air I can draw in each breath! I was a professional singer before all this began, and while I'm still not singing yet, I have begun retraining my voice, and it's certainly much stronger than it was a few short months ago.
Because of my food intolerance, and discovery that I am deficient, I am on a considerable supplementation regime. Although, none of what I'm taking could be described as "mega-doses." I'm keeping dosages lower, and spreading throughout the day when I can, because my absorption is currently poor.
I'm concerned that your doctors may have convinced you, either directly or by their lack of success, that your wife may be suffering from a rare condition. This may be true, of course, but I would encourage you to not discount the simple. The only, 100% sure way to test for food intolerance is with an elimination diet and a food journal. After sufficient time has passed, and if there is still a doubt, the diet may be "challenged" by adding back in the possible antigen. There is a list of several culprits.