Yes vitamin D is an important one for bone and joint issues and the impact of being low can be more extreme than you would think.  I hope you see a big difference going onto the extra vitamin D.  

I have hypermobile joints and they can get painful at times, but if I have low vitamin D they get worse.  I didn't know this at first and had a while there where my joints had got too painful to exercise, but the best thing to do to improve that is to exercise and build up the muscles around the joints to help hold the joints in place but I was in too much pain to exercise and it was a real catch 22.  It turned out I was low in vitamin D and that was making the pain a lot worse.  I started taking vitamin D suspended in oil every 3 months and while my pain isn't gone, it is a lot better since I did that.  

Supposedly most people where I live are Vitamin D deficient though.  For that reason, kids wear hats and sunscreen in childcare and school in summer but not in winter as we try to reduce the vitamin D problem by not wearing hats and sunscreen.  

Vitamin D deficiency is nasty on top of other bone or joint issues so I'm glad you've discovered that that was contributing.  You also have to consider other stuff like medications too as a lot of them affect stuff like bone density as well.