I'm no expert on running or injuries so I'll leave the meat of your question to someone else.
All I would say is don't neglect to rehab the ankle. Even though the pain goes there could be a weakness left there.
I'd do some balance work (maybe with a wobble board) and try to strengthen the ankle up a bit (I like those big elastic bands for this - dynabands?).
I'm trying to make this a part of my weekly routine. A bit of band work while sitting at my desk is pretty easy and I've just ordered a board which should make balancing exercises a bit more fun.
Hope it goes well for you