How to differentiate tendon/ligament/muscle pain

I have some bone structure issues in my right mid-foot/ankle that make it more unstable and flatfooted, which wasn’t an issue running until a bad sprain 3.5 years ago and subsequent overuse of an ankle brace causing the muscles to atrophy. This year I’ve been putting an emphasis on strengthening it, and consequently sometimes can’t tell if pain is just muscle soreness from the weak muscles getting work, or damage being done to tendons/ligaments due to instability. Short of medical imaging, is there a good way to differentiate symptoms of the different soft tissues?

For reference: dull pain, runs from the lateral malleolus down the length of the top of my foot when I supinate or point my toes. No swelling, no pain at rest.