Mystery solved

 My symptoms have gone away again after some detective work. 

I was writing my ND with all the details about them coming back, and started to type out the name of the Probiotic I bought yesterday and realized...oh...it's probably because of that. 

Sure enough, https://microbiomepost.com/a-lactobacillus-strain-worsens-symptoms-of-autoimmune-disease/

She confirmed that there are strains of bacterias that can worsen autoimmune symptoms. 
What I'd give to take a peek at what's going on in there with one of those miniature magic school buses.