I was recently diagnosed with very low Vitamin D. From what I've read, the "boney, achey" symptoms can take a long time to resolve. Apparently the pains are usually caused by microfractures in the ends of the bones, and it can take a while for them to heal. I've been advised to ensure I get plenty of calcium during the 3 months that I'm on the very high dose tablets.
Having broken bones some years ago, I can safely say that the joint pains I've experienced from the vit D deficiency are very like the pains of fractures.
I hope you start to feel better soon.