Sorry about the long list, especially for such a young person.
Might you have picked up some gut bugs when you were out of the country?
You have work to do on your digestive tract! Doing anything to support stomach acid, digestive enzymes? Clean up your diet so you are not feeding the bad gut bugs.
Have you tried modest doses of Iodine to support your thyroid? (high TSH)
Your adrenal and steroid sex hormones need support according to your list. Is your "bad cholesterol" low normal? Is that due to not absorbing nutrients in your digestive tract? There are inexpensive supplements that might help somewhat.
My recollection is that low vitamin D is more like 25 or so not in the 40s.
High homocysteine might be due in part to the low folate. The body also needs B6, B12 and choline to break down homocysteine. They are all in a multi B. Zinc and magnesium are also involved. Heavy metals such as mercury might be a factor; however I assume lead is not the biggest factor.
I'm not able to comment on much else. The good news is that there is plenty you can do, starting with cleaning up your diet and taking a multi vitamin. Taking some extra iodine, probiotics, digestive enzymes and apple cider vinegar with meals would likely help somewhat.
Are you sensitive to foods and drinks high in sulfites ?