As I have been training I have noticed that during my longer runs the area of my legs that hurt the most are generally below my knees. My calves and Achilles tendon area, so I have been jumping rope as a warm up to try and help strengthen this area.
I have also been doing some strengthening exercises like standing on one leg and with my hand point straight up, like I'm about to dive into the water I slowly bend over to tough something about waist high. This helps strengthen a lot of counter balancing muscles below my knees. Both these have seemed to help a lot for the short period in which I've been doing them.
I have found that it really helps to strengthen your core and counter balancing muscles that often get over looked when focusing on strength training.