I've already mentioned that my ankle's been playing up due to the right size shoes. The cure for this is running shorter distances and waiting until it gets better. Since I'm fixing this longstanding issue though, I might as well sort a few things out.
My toes are quite squashed from years of ill fitting (and just conventional) shoes. My 4th toes have started to straighten already, so now I'm using foam toe separators to push the hammer little toes out a bit further where they can start to work. That's having an effect after just a week, and making my heel and ankle ache.
I was aghast to find out quite how much suppleness I've lost over the years. I tend not to do much in the way of leg stretching, as it's caused me problems in the past. While I've been doing the Vivobarefoot ankle and tendon exercises though, I've discovered that the suppleness I had in my teens and early twenties when I did martial arts has long since departed. I can no longer kneel with my bum on my heels and the top of my feet flat against the floor - my thigh muscles won't allow it.
So I'm doing lots of stretching. Which makes for aching legs. But in the long run my legs and feet will work properly, as nature intended them to. I hope.