Make sure you are using proper form on the elliptical. Your feet should be flat, or as flat as you can make them, and you want to be pushing with your heels, not with your toes or the balls of your feet (the fleshy part below the toes). Consciously think about pushing down with the heel of your foot. Since the ball of your foot is hurting, it sounds like you might be pushing with that, rather than with the heel of your foot.
You also want to be standing up straight, not leaning forward, and sucking in your abs.
My Before and After Pics
"Decide what you want; decide what you're willing to exchange for it; establish your priorities, and go to work." --H.L. Hunt
"Life has hills. Set the treadmill at an incline."