Just to get a little more info from you, what is your running form like? What part of your foot strikes first? Do you make a lot of noise or feel a lot of impact? How is your stride length?

While some people can just go out and run and not have pain no matter what their form, for some people a detailed analysis of how they're running is just as important as a good bike fit. It could be that you don't "naturally" run in a way that is ideal for your body. I'm trying to guess what is causing the pain you're feeling...you may not need exercises as much as an adjustment in what you're doing.