The pain with running could be a running technique issue.
Have you had anyone look at your running mechanics?
Good to hear you are seeing improvements as you work with the elements in Becoming A Supple Leopard.
As Kelly has noted, “Injury to your central nervous system is a bummer, at every level. Tweak
your spine and you don’t want to move very quickly, much less lift
heavy weights, fight, or sit in a car for any extended amount of time.”
This may be a situation that takes time to get back in order.
Has your physio given you any suggestions on what to do?

Is your thoracic spine tight?
You may need to clean up your t spine position/mechanics.
You may have a downstream impact of an issue at the t spine.