Just over a year ago, I had the same issues you describe. Pain in my joints - knees, hips, feet, shoulders, elbows, it even went into my hands. No one could tell me what the problem was, though I had tons and tons of tests. My Dr put me on a low dose pain medication - and actually said it wouldn't help with the pain much, but it might make me feel better about it. (?!?!?) It didn't, really.
The pain was awful - dull and achy and bone deep. It would take me a half hour just to get out of bed in the morning because I couldn't lean on any of my joints or pull myself up. It was also very depressing.
I kept looking for answers and ideas. For some reason, I thought not eating gluten might help - so I tried it for a week. It didn't make a difference. I continued to research and have more tests - nothing helped. The depth of the pain was awful, and I tried to prepare myself mentally for a life of this much pain - not an easy thing to do!
For some reason, I tried the no gluten thing again last December 1st, but for the entire month instead. By the end of the month, my pain was decreasing. In January, it was almost totally gone. This year, I almost have forgotten, tho not quite - how much pain I was actually in. I can run up a flight of stairs now - and I'm happy every single time.
I do not know what went wrong. I don't know if I had this issue all my life and it just decided to freak out now, or if something caused it to turn over into pain. I don't know if there was some other medical reason for this and going gluten-free was a coincidence, but I doubt it.
I have never spoken to anyone who had this issue before, and I guess I wanted to say - I can relate. I really really hope this helps you!!