Vitamin D may decrease from certain medications such as certain anti-seizure, corticosteroids, heparin, certain antibiotics, mineral oil, and antacids; or certain disease states such as celiac disease, Crohn’s disease and Whipple’s disease. Insufficiency may cause symptoms such as bone loss, osteomalacia (in adults), and impaired Calcium absorption occurs due to very low levels of the vitamin. You did not mention your Calcium levels and suggest getting it checked. An intake of Vitamin D 400 IU is sufficient for your age. You should not go over that amount in supplementation. 2000 IU is the tolerable upper intake level for adults; however, you can be at risk for toxicity (weak muscles, weak bones, excessive bleeding, and kidney stones) if you consume supplementation plus large amounts of fortified milk / dairy products and fish. Vitamin D is available through our foods - Fortified milk, breakfast cereals, egg yolks, fatty fish, fish oils, and the sun. Sit at a window with the sun shining in for about 1/2 hour (few times a week) and that will help you get enough Vitamin D. Suggest you find lower the Vitamin D supplement with less Vitamin D or none at all to help lower the amount of Vitamin D in your system. Suggest finding out the cause of the deficiency to treat it.
Have they re-checked your ferritin and B12 levels? 46 is fairly low - not below what the labs consider normal, but some doctors say you can be symptomatic below 50-70. Have they tested you for Celiac disease recently? A lot of what you describe fits (I saw your post from 2008 on your profile) - the fatigue, hair loss, cognitive difficulties, pins & needles, low BMI, vitamin deficiency... Certainly worth a blood test, and yes, the result can change over time. I'd ask them for the full panel, not just the single test.
2,000 IU may be the daily UL but from what I understand, it's standard practice for doctors to administer mega-doses when a patient is found to be deficient.