If you go to a decent running store, they'll record you running on a treadmill. They should show you what your ankles are doing so you can pick shoes to support your feet. Most people aren't biomechanically sound, the ankles roll in or out a bit, this can be mitigated with shoes and inserts.

My ankles roll in a lot, with out a fair bit of support, my knees kill me.

Also, muscles recover quick but tendons take forever to heal - you're not running from a lion, so you can take your time and experiment with what works for you in a safe way. (it sounds like you are, so good for you)