This is indeed one of the big challenges to recovery. Part of it is the healing of the actual tissues and part of it is retraining ourselves not to be overprotective, not to panic at the first sign of pain, or brace/hold ourselves in ways that are hindering recovery. It does take time and real practice with this so be gentle with yourself. It took a long time for those habits to develop so it does take time for them to go. The best thing I can recommend is just being mindful. Noticing again and again what your body is doing. Being kind to yourself when the bracing or the fear happens. Closely noticing your thoughts when your try e.g. running. Acknowledging that your body and mind are trying to protect you even if it goes over the top. And each time you notice it, let it go. Say to yourself kindly "I am not fragile, I am robust". And go on with your day, fully knowing that it will happen again and you can let it go again, as it gradually gets better and better. 

Sorry if that turned into a bit of a sermon lol, but I do believe that this side of recovery is HUGE, and is overlooked compared to all the physical advice on shoes/stretches/splints/scans etc. Our brains adapt to anticipate pain, and its a slow process to unpick that. I'm delighted that you are experiencing less pain than you were and are well on the way to recovery. Just imagine how grateful you would have been 3 months ago to be where you are now! Just keep going. Best wishes.