Wow, I am now also on an epic journey recovering from bacillus subtilis, I'm sure. My health has had the exact same decline since taking a probiotic containing that two years ago; it took me a year to figure out that is what did it.
Still working to get out of it. I have had great success with kyolic garlic, Allimax, Bio K and homemade kefir, but I know it is not gone. I still frequently suffer from gastritis, indigestion, liver issues, adrenal issues, sinus issues.....
I just tried l reuteri for the first time today; I've been terrified to try it after having my health completely dismantled from a probiotic. I don't think of bacillus subtilis as a probiotic anymore though, I think of it as a spore that has taken over my gut.
Where are you at these days?? Did it get any better?