Pain in my. . . *%#@

I have been running and it has slowly become a problem. I didn't notice much a few weeks ago, but now it is almost unbearable. When I run I am getting a lot of pain/discomfort in my feet. I am not sure how to remedy this. I searched it online and it mostly suggested adjusting/changing foot wear. So perhaps my Nike's just aren't a good fit for my feet, or my stride? I pushed through the pain today. . .literally, my calves are pretty sore from running in my vibrams cuz they give my legs a MUCH better workout!!!! Until I can figure out this foot pain thing I am not sure what to do. I don't want to quit running because my endourance is improved so much. Any suggestions are welcome.