Misdiagnoses of neck strain meant the costochondral separation was not treated properly in the acute phase. after two years, is there hope to heal?

Prolotherapy: You can heal from costochondral injuries with specialized injections to promote ligament healing and stability. Perhaps the back pain and headaches are also part of the picture. Seek an experienced physician in prolotherapy and manual medicine techniques to evaluate you.

Yes: Interesting - presumably your "neck" pain is low and in front, and the costochondral separation is high on your chest wall. Keep in mind that the treatment for a costochondral separation is essentially the same as that for neck strain - time, pt, localized treatment such as e-stim, and nsaids, so you may not have lost anything from the misdiagnosis. Consider steroid injections and home tens.