Try gluten free for a week!
"three yeast tests"
What type of tests (a culture?) and where was the swab from? There are microorganisms everywhere in the world, including candida in stool. A yeast infection is more about an overgrowth, not a presence of absence of.
There are different subspecies of candida.
I'd also mentioned that some bacteria behave like yeast. The GI gas doesn't come from nowhere. I think that's a central feature.
The flareups could be from what you eat. I'd keep a food diary.
Consider this: microorganisms communicate with each other. A flareup in the intestines can release growth factors that travel through the bloodstream and tell others of the same species to get active. That could explain the nose.
Neutrophils increase from bacteria or yeast. Or even from the coating (LPS) of dead bacteria. Leaky gut from GI microorganisms can let many things through into the bloodstream, not just organisms but also biochemicals and proteins that can cause systemic inflammation and the resulting tiredness/malaise.
What was the cream that helped? Topical antihistamines or steroids?
Elevated ANA by itself is not necessarily proof of anything. In fact, some rheumys discourage internists from giving ANA tests without very good reasons, else a low positive just provokes needless worry.
On the other hand, there is such a thing as "sterile inflammation" in which mast cells are usually involved.
Are you taking 5000IU vitamin D? There's no harm as far as I know, unless you are also getting lots of calcium which then gets hyper-absorbed.
Yes, low vit D is associated with autoimmune and auto-inflammatory, likely since D is an anti inflammatory.
Are you sugar free?
Yes, I think you are quite correct about the yeast. (Else it might be a bacteria that behaves like yeast.)
A simple elevated ANA is not enough to suspect autoimmunity. But the yeast infection can stir up your immune system, put it into fight mode, and cause a lot of your symptoms.
Have you tried to control the yeast? If not, we can talk about that. You mainly want to kill it and/or starve it.
Do you have a family history of immune system diseases, even severe allergies?
Do you flush a lot? Red skin.