Hi Sam,
Have you considered Tibialis Posterior dysfunction. I had a football player who suffered a kick onto the inside of his ankle. He was treated for medial ligament sprain but did not improve over a number of weeks. As a student at the time I researched to discover any other possibilities and discovered tibialis posterior dysfunction. I strapped his foot and he was able to play with no symptoms and gradually he was weaned off the tape and returned to normal play.
Tibialis posterior is involved in maintaining the arch of your foot. With a kick to it, even though you don't tear the muscle, you effectively stop it from working properly. Due to this you then start to pronate more (loose the natural arch in your foot) which in turn stretches the tendon which stops it working properly - so in a big cycle!. The aching is a sign that the muscle is trying to work to hard to maintain the arch but isn't strong enough to do so. This becomes more noticeable with quicker, unexpected movements.
The initial thing to try with it is a taping technique called "low-dye taping" which will support the arch of your foot and therefore take pressure off the muscle and should help with the aching. There are exercises that you can complete, but as you've had this for so long, they may not be effective. So due to this, if the taping technique works, then an insole would be the best thing to go for - however, I would get one custom made if possible. Before that, ensure that your shoes are supportive - ideally a trainer with a good arch support is best, rather than a smart/dress shoe. Also try not to walk around at home with no shoes on, especially if you have hard floors
Hope this is some help to you.