I am on the fly and will come back with a more thorough reply but a few things. . .
Yes, I am on a sort of hybrid paleo/Mediterranean/anti-inflammatory diet. I do not eat any grains, which made a huge difference for me all the way around, but I do eat yogurt (all other dairy I avoid). It's been quite a journey to figure out what my body does and does not tolerate and it certainly sounds like your experience is similar in that regard. I am still continuing to learn and sort things out; luckily these days I am getting foods back versus the opposite.
It does sound like your SIBO hydrogen breath test was botched unfortunately. Those sorts of tests are kind of iffy to begin with so it is never a bad idea to re-evaluate periodically!
Reading your signature, I see that you have noticed some improvement on a low histamine diet? Out of curiosity have you ever had food allergy (IgE) skin tests (aka scratch tests)? If so, do you remember if you might've reacted to the 'control'? The control is typically just concentrated histamine, and thus may shed some light on a possible connection.