If there is pain when you're running, you're doing something wrong. Slow everything down and make adjustments to your form until the pain stops. Make sure you're landing lightly and directly above your feet. Have a look at
www.chirunning.com for information on correct body position.
I had started having injury problems, and this was as a fit runner, until I learned correct form and now I have ditched the cushioned shoes and run in Vibram Fivefingers without any pain at all. It's wonderful and has brought a new enjoyment of running. It takes time and effort but, as with changing to a raw foods diet, it's worth it.