Yes, the probiotics, taking high doses over a period of time, healed my leaky gut. The type I take are "3.0 Billion CFU's per capsule". I took one in the morning and one at night. I still take them. I've read that gluten issues "leech", or suck, vitamins/minerals and our "villi" is always going to be struggling to keep up. Vit. D is one of those. I'm not at all an outside kind of person, so I take extra D in pill form. But they say 10 minutes in the sunlight is good for a day's D. And I help my "villi" by taking the lactobacillus acidophilus. I would suggest the next time you go to the doctor and have blood drawn to ask them to do a work up on your vitamin/mineral levels and then find ways to boost those.
One more question....I went back and scanned your post again. Is there, by chance, a non-glutenfree person in your household? I'm the only gluten-intolerant person in my household (at the moment). MOST of my cooking is just whole foods, naturally glutenfree. But occasionally I fix things that I do both....glutenfree AND normal. Like spaghetti nights or something. And they do for themselves all the time in MY kitchen, lol. They TRY hard to be aware but I've seen them lapse in remembering things I need for a non-contaminated work area. So I'm vigilant about washing down my counters and surfaces they touch A LOT.