I just saw this thread. I have also had trouble with taking Vit D. Same thing - muscle and bone pain increase along with general flare and malaise. Also had a level at 4. I do have Celiac, also - and have been on the gluten free diet for a little over a year.
My docs can't explain the mechanism that causes Vit D to feel so "toxic". I do think it has something to do with not being able to absorb it - and this may be where the celiac comes in. I was told not to take "naked" VitD, let alone the 50k doses that I had been Rx'd before. So I've been getting my vitamin D in a calcium/mag/D supplement. Taking it 4 or more times a day. It hasn't caused the same trouble that just plain D, in any amount caused. Will be getting a repeat level done soon. I also know it's important to have a calcium blood level taken as well when taking these supplements.
Good luck to everyone dealing with this....it is frustrating!