Hi, sounds like you have been going through some very frustrating diagnoses. I have been having many of the symptoms you described and about a year and a half ago I was diagnosed with Fibromyalgia and Chronic Fatigue Syndrome; that after years of complaining to my doctor off and on of symptoms. I was not happy with my diagnosis (I too have an extremely hard time absorbing Vit D except through UV exposure and a multitude of vitamin deficiencies which were never addressed). After having years of chronic constipation, even when trying everything natural and unnatural to be regular, I heard about being gluten intolerant and decided to pay attention to my reaction to gluten. I didn't really take it seriously until the Mayo Clinic listed "Decreased Dental Health" as one of the symptoms (I had been having pain, tooth loss and infections for over a year which I had never had before and I attributed it to my low Vit D). As soon as I read that symptom I stopped eating anything with gluten in it and low and behold 3 days later the pain and infection disappeared (however it comes back when I have a cross contamination issue).
For me being gluten free is less frustrating that it can be for most people because my system reacts very violently and immediately to exposure. I bloat and become nauseated within minutes and spend 1-3 days with "Fibromyalgia" symptoms along with constipation/diarrhea , pain and fatigue. As hard as it is to not eat my favorite crackers the reaction to it keeps me from doing it.
I do have infertility (did have) but it is from a congenital adrenal disorder so I know it is not related. I worked with an endo/fertility doctor and have a teen daughter. The Vit D like you is very frustrating even when taking high doses; when the Mayo Clinic told me I had Fibromyalgia and very low Vit D (7) I was told to take 3500 a day and I shot back that I was already taking 5000 a day. I'm also anemic and was told my RLS is from low iron ----but honestly most of my symptoms from all of what I have been diagnosed with dissipate when remaining gluten free (even a little cross contamination makes me violently ill). Today is a day that is not good all because I had a bite of rotisserie chicken and potato salad (modified food starch!). I won't be doing that again.
Good luck to you and I am glad that I found this website so I have others who understand and can relate to. It is good to hear that I am not making this all up in my head and these weird things aren't just happening to me!