Suggest Treatment For Strange Pain In Legs

I have recently been experiencing a strange pain in my legs when I go running (particularly at the joints from the ankle (which are in the most pain), at the knees, and at the point where my legs connect to the rest of my body (the upper thigh region)). I normally run on sand and asphalt which have been fine for me for the previous years. I have running shoes (fairly new) and I usually run between 1-5 miles depending on what I am training for that day (endurance/speed). I have not made any sudden jumps in my intensity (which is traditionally very high) or the distance ( I have slowly over the course of the last year worked my way up from 1-5 miles) I run. I am conditioning myself for The Citadel the Military College of South Carolina so being picky about the surfaces I run on cannot be an option (they run on all terrain). About 2 weeks ago I experienced a strange and sudden pain while I was running off the side of the road (fairly early on in my work out) I walked back home and the pain slowly dissipated over the course of 48 hours. After about two weeks off (thinking I should let myself heal) I tried running on the sidewalk today. I made it about 10-15 minutes into my exercise before the same exact pain returned. I am not sure what to do. Thanks, Dylan P.S. I stretch before and after runs, and also ice my ankles.