Painscience.com and Hargrove's "A Guide To Better Movement" are pretty good for a model of predictive processing and the roll of the nervous system in chronic pain and movement. I still don't feel like I have a good model of bone and joint health in general, however. Eg, I'm currently nursing a flare up of patelo-femoral pain in my left knee. I've done a number of things over the past few months to deal with it, with some success, including buying and reading Painscience's book length patelo-femoral tutorial. Recently I've had a bit of pain in my foot, possibly in the tibiocalcaneal or tibionavicular tendons. I find that even though I now know a fair amount about PFS and the way the nervous system processes pain, these models don't generalize well to sporadic, idiopathic pain in another joint.
Possibly the answer is: "lol that model doesn't exist", or "lol wanna get a phd?" but if there are good resources, I'd be an eager consumer.
A sub-question that I'm particularly interested in is: what, if anything, is know about the relationship between base line muscle tone and joint issues? I have good reason to think my baseline muscle tone is higher than average.