See a physio and get yourself checked for your biomechanics.
I only went after I tore my Calf only to find my hips, knees & ankles weren't working correctly & now I have a range of exercises to correct them. It's working because I did a Half Marathon last week without aftereffects.
Strangely I'm not to do any of the stretching exercises within half an hour before or after running, so warm up by starting gently, and cool down by incorporating a short walk at the end. This may be individual to my situation, so my advise is get profession advice (my physio says it would have be best to see her when I restarted exercise in 2010 and not wait until I'd damaged myself this year).