Try a salt push (1/4 to 1/2 tsp. of a quality sea salt in 1/2 cup warm water, drink it down, then chase with 12–16 oz. glass of water). Can repeat after 30–40 minutes if needed (do a search on "salt push" for more details). That usually helps me with deep into the bone aching pain. And also combine with iodine supplementation with the companion nutrients.
I'm just guessing, but it sounds like your body is holding on to a lot of toxins, and the iodine supplementation regime will help ... but it's going to take some time.
Also, how is your sleep? If you're not getting quality sleep, your muscles won't be healing up like they should and other body maintenance things that happen in deep sleep won't be happening.