Skullbasecancer4, I was just diagnosed with Gene Mutation and my body does not detox nor does it absorb Folates (B Vitamins). I inherited 1 gene from my mom and 1 from my dad and was born with this. This explains a lot as to why I have so many upper respiratory infections and was my Mom's sickly child. Perhaps this is something she can be tested for.....Our Western Medicine do not usually check for this so you would have to go to an Integrative Medicine Doctor. Someone that "thinks outside the box". It is out of pocket for me and not cheap, but, I am encouraged that I'm getting to the root of my problem and chronic infections & other health issues. I'm putting your questions in numbers:
1) Yes, there is a correlation in autoimmune diseases and infections.
2) I went to an infectious disease doctor after Covid which left me with mucousy saliva in back of throat (which I still have) that would not go away and she didn't find a thing. No offense to doctors and specialists, but, they are still learning about Covid and how to treat Long Covid.
3) I see an endocrinologist (I have both thyroid diseases), rheumatologist (I have borderline Lupus or mixed connective tissue disease....can't give me a definite answer), I see my Primary Doctor and ENT for recurring sinus infections and I see a Pulmonologist for chronic asthma, bronchitis and pnuemonia since having COVID.
4) Yes, I was diagnosed with Long COVID and yes, it has triggered more infections, especially sinus infections, asthma/asthmatic bronchitis & I am more prone to pneumonia. I never had pneumonia in my life until I got Covid last year.
5) If she goes to a Rheumatologist and her inflammation markers are not high enough, most of the time, they cannot give you a definite answer as to what she has and will say it is borderline and to just watch for symptoms.

I am praying for you and her. I know this is so long and drawn out for her and you and frustrating. There is hope. All my love & prayers. Keep me posted.