Where I have had muscle/joint/soft tissue pain, it’s usually linked to wonky gait arising from MS damage, so it’s easy to see what has caused the problem. Once the business of getting about becomes awkward and stilted, soft tissues get pulled and squeezed and pushed in ways they don’t like, and that’s when the trouble starts. That has been my experience. I have not had the kind of things that you describe.
Yes I too suffer with joint and muscle pain; after requesting a referral to a rheumatologist via my Neurologist, I was also diagnosed with Fibromyalgia. Apparently this is what is contributing to my pain.