Nick I don't mean to keep asking you questions but to be honest none of the other "experts" gives me satisfactory answers. My foot/ankle is marginally better than it was but it still is very stiff in the morning and during the day when sitting on the train or at my desk. It is definitely not the Achilles tendon but on the inner side of the ankle into the arch/instep and inner heel. Are there good stretches or strengthening exercises I could do to increase flexibility of these ligaments so I can get back to pain free running (and walking)?
Use the towel eater exercise. This works muscles that rarely get worked well enough.
Have I given you slow heel raises to do? https://www.youtube.com/watch?v=YiesZvSVa7c
Work both of these pretty well. If these don't do it for you then you may need to see a physical therapist that can provide manual therapy to your ankle and foot.
Let me know how this does for you.
I'm glad you're pleased with my past answers.