@greenfish – First a disclaimer that I am not a doctor neither therapist, but I can give you my experience with an injury that seems very similar to what you are describing. I experienced the same symptoms, I didn’t even need to run it was enough just walking for the pain in my fibula area to develop. My symptoms started in 2009 after meniscus tear injury. After recovery I started with exercises and to my surprise this pain in my fibula area appeared for the first time. It stayed with me for about 6 years. I have seen countless number of doctors and nobody with similar symptoms. Eventually, I ended up in Mass General in Boston where they told me my fibula attachment is loose. I could have done a surgery to tight in fibula, but such type of treatment was suggested if I do a lot of sports. I guess there was no guaranties with a surgery. I like sports however I was never professional, but as I mentioned, in my case this problem was many times in a way of my usual daily activities, forget professional sports. In anyway, I started hamstring strengthening exercises and also stretching of IT band (peroneal nerve area) which helped me. After all this time and for about a year now I didn’t experience problems, but as I mentioned the most I run is 5 miles. I concluded my research with assumption that subflexion of fibula is irritating peroneal nerve that is in close proximity, thus the pain. I hope this helps you somewhat.