Only your left foot is hurting.  Are your feet the same size (length and width), if not take a look at Size matters when selecting shoes - Asymmetrical Shoe Size. A simple method to confirm that your feet at the same foot size, is to put your heels to the wall, heel together, toes together and look down at the toes to see if they are the same size.

Damien Howell PT, DPT, OCS - www.damienhowellpt.com 

I think it's your shoes.

If you are only running in one pair, you are repeatedly stressing your feet, ankles, knees and hips the same way everytime you run.  I strongly recommend that you go back to the store and get properly fitted in another pair of shoes that are different -- even a different brand.

You might also want to try neutral, or cushioned, shoes.  The location of your foot pain suggests that your shoes are working too hard to keep you from pronating, thus pushing your left foot out.  DON'T PAY ATTENTION TO STANDARD SHOE GUIDES!  I have low arches, yet have had far more trouble wearing stability shoes than neutral.  Further, my favorite shoes, Mizuno Wave Rider 13s, supposedly don't have enough cushioning for me due to my size (Clydesdale).

In the meanwhile, try icing your foot during the day after you run.

Good luck!