Zizzle,
Wow! You ask some tough questions. I wish I knew the answers. (I can answer some of them, but I can only make an educated guess at others).
Actually, GMO wheat does not exist, (at least not in the conventional sense). The only wheat seed modifications that have been made since the dawn of the neolithic period, have been by selective breeding, though admittedly, most of them have been made in the last 200 years. Technically, selective breeding is a form of genetic modification, but it does not involve any laboratory-based gene splicing, obviously - instead, it takes advantage of natural mutations that occur by evolution.
OK, this part is just my opinion:
Yes, I agree that something besides just gluten-sensitivity, (and other related food-sensitivities), are at play here. I have a hunch that a huge part of the problem is that our immune systems have been bombarded for the past few decades with increasing numbers of "chemical foods", rather than real foods. Items such as artificial sweeteners, natural sweeteners, (that are not really natural, such as corn-based sweeteners), chemical preservatives of all descriptions, emulsifiers, (made from soy, and who-knows-what-else?), synthetic this, and synthetic that, isolated food components, (rather than whole foods), that we were never designed to eat, such as inulin, natural flavorings, starches, polyunsaturated this, and hydrolyzed that, etc., etc., on top of the issues caused by grains that we were never evolved to digest, and exacerbated by mycotoxins in grain, all probably contribute to the problem. And on top of all this, all these chemical and nutritional "experiments" that we are regularly conducting, are bound to cause changes in our gut bacteria populations, and most of those changes are probably not for the better.
The food manufacturing industry has somehow convinced us, that rather than eating real food, we should eat an assortment of chemical ingredients, tailored to deliver the specific nutrition that we need.

The net result has probably resulted in our immune system becoming overwhelmed with issues that it was never evolved to handle. Our immune system evolved on whole food, not "designer" food.
In paleo times, by the time a baby could walk, their immune system had already most likely been exposed to just about every possible threat that existed in the prevailing environment. Today, we continue to bombard our immune system with new issues on an almost daily basis. New "food ingredients" are continually being developed, (hundreds - maybe thousands, are developed every year, though not all of them are adopted), and where are they developed? In laboratories, not in gardens or forests or fields. Our immune systems were not designed to deal with threats developed in laboratories. IOW, IMO, our current problems are probably due to a myriad of causes - we're simply flooding our body with more junk, (junk created in laboratories), that it can deal with, on a continuing basis. At least that's how I see it.
Zizzle wrote:And why are celiac patients developing MC despite strict adherence to the GF diet? Something else must be at play here...
I don't recall the exact numbers, but research shows that approximately half of all celiacs are not 100% faithful to the diet, either due to occasional or frequent cheating, or because of failing to be diligent enough in label-reading, etc., or from accidental exposure due to cross-contamination, or incorrect labeling, (which happens far more often than most people realize). That makes them all vulnerable to developing other autoimmune issues, including MC. In many cases, I'll bet the damage was already done before they were initially diagnosed with celiac disease, because of the poor diagnostic rate. In some cases, both diseases are diagnosed at the same time, and in others, it probably takes a while before the additional food sensitivities became "mature". Many doctors stop looking, once they find either celiac disease, or MC, so the other disease isn't discovered until later, when a patient fails to respond to treatment. That's probably especially true when celiac disease is diagnosed first.
OK, this part is fact:
I agree that mycotoxins in grain are probably a part of the mix that I described above, and they are definitely on the increase. 20 years ago, aflatoxin was a seldom-encountered problem, and the other mycotoxins were virtually unheard of, outside of academic halls. Today, it is a very frequent problem in many parts of the world, and the concentrations of not only aflatoxin, but fumonison, zearalenone and others, are showing up in grain fields in increasing concentrations, with increasing frequency. Their presence is monitored and regulated by USDA, and state regulatory agencies, of course, but we all know that most government regulatory agencies are far from efficient.
Zizzle wrote:If we want to avoid these mycotoxins, are they primarily found in stored grains? Is fresh corn OK? Does rice harbor the same levels of fungi?
Most mycotoxins develop in the fields, while the grain is growing, or while it is maturing, but in some cases, it can also become worse, during storage, if storage conditions are not correct, (IOW, if grains is stored with too much moisture, the problem can increase). Yes, immature corn is safe, (aflatoxin, for example, cannot develop until the grain dries down to below roughly 18% moisture). Fresh corn, (roasting ears), should have a moisture level at least up in the 40 to 50% range, so it is perfectly safe. I'm not aware of any mycotoxins that commonly infect rice. Corn, grain sorghum, (milo), wheat, (and related grains, such as barley and rye, spelt, etc.) are vulnerable, both in the field, and in storage. (Wheat doesn't normally develop aflatoxin, or fumonison, but it can develop vomitoxin, zearalenone, etc., if growing conditions are unusually moist).
It's possible for rice to develop aflatoxin or fumonison, but due to the fact that rice grows in water, and the fact that it's a relatively expensive crop, so that proper storage conditions are universally maintained, IMO, the odds of finding any rice contaminated with a mycotoxin, are close to zero, (at least in this country). Admittedly, I haven't checked out the statistics, but I see no reason why mycotoxins should be anything more than a theoretical problem, with rice.
As far as I am aware, no normal cooking process can destroy any mycotoxin, (without destroying the food, in the process), because very high temps are required, for a significant period of time. A strong solution of clorox bleach will neutralize it, as will exposure to ammonia, at high pressure, and an elevated temperature, but since that will turn any grain or seed product black, it's not a practical solution.
Zizzle wrote:Is any grain safe? Do dry beans and legumes also carry fungi?
The first food item in which aflatoxin was discovered, is peanuts, (a legume), and aflatoxin is still a problem with peanuts. Hopefully, the regulators do a decent job of minimizing the risk, but I'm pretty sure that a fair number of contaminated peanuts reach market, because they're uniquely vulnerable to fungal growth, due to the fact that moisture control is more difficult while they are still in the shell, (they're harvested in the shell, and usually stored that way, until final disposition). (Never eat a moldy-looking peanut.) Cotton is not a legume, but cottonseed is another food product that often has a serious aflatoxin problem. It's claimed that the oil should be safe, but we all know how shaky a similar claim about soy protein not existing in soy oil, turns out to be, for anyone with MC.
I'm not very familiar with the bean business, but yes, dried beans are vulnerable to mycotoxins, if not stored properly. In fact, mycotoxins are even found in coffee beans, but proper roasting, in an oven, at 200 degrees C, (400 degrees F), for about 15 minutes, will usually bring down the level to a tolerable percentage.
IMO, rice is probably the safest common grain, from a mycotoxin risk standpoint. Rice should inherently have a very low risk.
Zizzle wrote:All my autimmune issues started during a post-partum period marked by a bladder infection and 4 rounds of mastitis and LOTS of antibiotics. Could this be the trigger and not the pregnancy at all?
I'm back to simply stating an opinion, here, again, but IMO, the multiple doses of antibiotics are probably much more likely to have caused long-term autoimmune problems, and gut bacteria population issues, than the hormonal changes that occur with pregnancy.
One other thing comes to mind, and this is just thinking out loud, but one of the biggest sources of gene alterations are viruses. Environmental effects, such as gut bacteria, stress, (possibly vaccines), and probably a few other undiscovered influences, can cause epigenetic changes that result in the triggering of genes, but viruses can alter the genes themselves. I suspect that viruses may play a much bigger role in our health, than the medical community understands, and I certainly don't claim to know much about it, either.
I hope this helps.
Tex