I have gone through your question. I can understand your concern.
You have vitamin D deficiency and you are taking supplements.
Your x ray
is normal so no any bone lesion. It may be due to arthritis
Your calcium level is high normal. However you should check your ionised calcium level once. If it is high then check your parathyroid hormone
Then you should take treatment accordingly.
Hope I have answered your question. If you have any doubts then feel free to ask me. I will be happy to answer.
Thanks for using health care magic. Wish you a very good health.