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Could be sulphites, although I've read in multiple places that getting over Gluten can takes up to two years! It's funny too because I stopped eating gluten about two weeks ago and about a week in, I got REALLY sick. Like sicker than I had been in years. I wonder if it has to do with my immune system finally getting back to some form of normal. Ever since my symptoms started, which I must say are only partially overlapping with yours (mainly loose stools and nausea) I never really got sick, and when I would get sick it would come on so slowly and then drag out even longer, almost as if I wasn't really sick, but still fighting something, chronically.
The rest of the time, I wouldn't feel sick, but I wouldn't feel healthy either. I always had headaches, nausea and no digestive distress, but never really 'normal' stools.
Since cutting out gluten(and dairy) I must say the headaches are almost completely gone and my stools are more normal than I ever remember.
I don't think I have Celiac, but I am definitely sensitive to something that is in my everyday diet.
For you and me, let's minimize sulphites, gluten, dairy and soy. Fact is the foods that contain these are generally highly processed and no where near as healthy as they are advertised to be. Not to mention that manufacturing methods (something you come to realize doesn't belong in the same sentence as 'food' anyyway) have gotten much worse.... more preservatives, more chemicals, more "nutritionally enhanced" products everywhere.
Last thing, if you want to see if Gluten affects you, you CAN NOT eat Gluten Free products either, Gluten Free just means less than 20ppm and most of those products will actually contain some gluten, which I believe is enough to cause us not to heal.
If you really want to find the source, don't eat anything that even has a label, it's not natural and not fit for human consumption. We've been brainwashed (even doctors) to think that we can eat anything we want whenever we want... heck maybe we would be immortal if it weren't for all the garbage we (love) force our bodies to process...