Top of Foot/Ankle Joint Pain

I've been running (after recovering from ITBS injury) for a couple months now, but only recently have I been increasing my miles.  The most recent injury or issue I've encounted is this pain on the top of my foot, but in the nook of my ankle if that makes sense, right below the knobby ankle bone.  When I would run, it almost felt like something was being pinched in that area.  When it first started coming on, I thought I had my shoes laced up too tight.

I went to see my PT, who solves all my running issues of course--seriously!  After checking to make sure that my tendons were all okay, he said that most running injuries have to do with range of motion, or lack thereof.  In my case, with the build-up of miles I was running, my calves were getting really tight and cranking down on my ankle.  Thus the pinching feeling.  All I did to get rid of the ankle pain was do 2 stretches he recommended to start stretching my calves--not necessarily my whole hamstring (which probably wouldn't hurt to do but wasn't the main issue).  Specifically, he had me stand, facing the wall, put my hands on the wall in front of my with one foot forward and bent at the knee with the back leg stretched back.  He told me to turn my back foot in slightly in order to get at all the muscles in my calves, then just bend the front leg forward to stretch. 

The second stretch was the same thing, only bring the back foot closer to the wall (so the distance is less between the front and back feet) and then bend the back knee so you are stretching your calf but bending at the ankle.  It feels really weird, but it totally works.  I also stretched my calves by hanging my foot off a step (or a curb works fine).  My PT said that the hanging off the curb stretch is pretty hard core and the other ones should be fine, but what can I say--a bit of an overachiever and I wanted that range of motion back! 

Now I don't have any pinching in my ankle or any top of foot pain.  I also ditched my orthotics at his suggestion; I thought long and hard about this, and I determined that the orthotics could be restricting the range of motion my ankle needs while running.  So far my runs have just been getting better, even without the orthitics, and I've continued to increase my distance.