I sort of know what you mean. I am going through retraining my ankle/foot because of an injury. One thing you might try is a wobble board, and just sitting and getting your ankle to evert and invert (tilt in and out) to see how well you can do that. It sound unrelated but I had a similar problem and because I lacked the neuromuscular control, it just started from there.

Do you have access to a physical therapist? I would go to one since you were injured. Especially one that knows about cycling...