I am not a physiotherapist but am about to be a student in Physio, and I also run and workout. The laymen term for what I think you have is " shin splints". All it really is is inflammation on under your tibia. when you press on the inside of your lower leg, it hurts right? So when you stretch, try sitting on your butt and feet together, legs straight out, but actually point your toes out. Thats how you stretch the top part of your lower leg. Do this and use an anti inflammatory sparingly, along with icing after running, and I really think it will go away. The best way to ice for this is to do what alot of internation football players do. Do an icebath It's painful but the pain relief is amazing, and there is empirical evidence for it. Most ATC will say that. So try an ice bath( for the lower leg) and you will be a lot better.