Chronic knee pain w/ other joint issues

My info: 29, female, 5'5'', 117 lbs., white. Please give me any advice or thoughts, I have seen many practitioners (primary, PT, ART practitioner, orthopedic doctor, chiro, acupuncturist) about this issue.

Ran marathon three years ago, began PT for IT band issues. Stopped running, knee pain continued along with extreme hamstring pain near back of knee. Have had chronic daily pain along inner right knee near top inside of knee cap for at least a year and a half, along with hamstring pain originating from connection at back of inner knee on same knee. I foam roll daily, largely stopped exercising for 9 months in case it was overuse (was working out 5-7 times a week doing yoga). MRIs 9 months ago on both knees showed no damage. Orthopedic doctor who ordered those MRIs suggested I have extremely loose connective tissue during the exam and asked if I have ever had genetic testing performed (I have not). Prior to this MRI (about a year ago) my primary care doctor tested me for autoimmune diseases (Complete Metabolic Panel, ANA screen w/ titer & pattern, CRP, ESR) all of which were unremarkable aside from a barely out of the range Mean Platelet Value at 11.6 fL, which I was told was normal. Vitamin D was low at 23 ng/mL, I have supplemented but not retested.

I have hypermobile joints and have also been having pain in my elbows, wrists, and fingers but not to the degree of my knee. I have not slept through the night in over a year because of constant need to rotate, sleep with a pillow in between my legs, and not sleep on my stomach because it puts too much strain on the back of my knee. When I am awake, I am constantly having to move my leg because any amount of time in any position, bent or straight, I have pain along the side of my inner knee into the quad or sharp pain behind my knee into my hamstring. I am not on any pain medication and have not been on any throughout this process.

What should my next steps be? What type of specialist would test for connective tissue disorders and how might that help me? Could this be nutritionally related (low vitamin D/other deficiencies)?

Possibly/maybe not related: High cholesterol, injury to to the pleural lining from a coughing too hard about 3 years ago (is this typical for someone in their mid-twenties?), and changes in my menstrual cycle (two periods in one month three times this year, normal U/S and neg preg test).

ETA: I almost forgot. A little over a year ago I had a sudden pain my neck like when you sleep on your neck wrong. However, it developed in the middle of the afternoon and did not get better for over a week. I went to the ER after days of not sleeping and a feeling of neck instability and they gave me tylenol and patted me on the head and sent me away. I continue to have a loss of range of motion in my neck since that occurred.