Sounds like generalized inflammation could be part of the problem. You might try cutting out processed foods, anything with sugar, white flour, etc., and switching to unprocessed fruits, veg, legumes, and fish/meat for a month, and see if that helps. It certainly can't hurt.
Also - how's your indoor environment? Do you have good air filtration?
I suffered for a few years with massive generalized leg and hip pain. This was after moving into a new place with brand new carbonized bamboo flooring. Shortly after moving in, I could not walk, bike, stand, sit, or sleep without pain. The first 2-3 years were the worst, especially in winter when windows were closed. Things gradually improved and last summer we moved. I'm now pain-free.
I strongly suspect that I had a bad (inflammatory) reaction to the formaldehyde off-gassing from the floors.
Also, keep up the good work with exercising, and stay active. Movement is like oil for your joints. Being a couch potato feels great when you're doing it, but is bad for you in the long run; exercising feels bad when you're doing it, but is great for you in the long run.