Hi, sounds like you are developing a Morton's neuroma. You might consider getting custom insoles, REALLY stretching your calves and feet after running, and doing deep foot massage (like when you're watching TV or something) where you work your thumb deep between all the joints in the ball of your foot.
What's happening is the nerve that runs between the fourth and fifth toe is getting irritated. Eventually, it will develop scarring that will make it even harder for it to pass through the bones on the ball of your foot, and exacerbate the problem. It'll start to feel really painful.

The massage might work to reduce the scarring, and spread apart those joints.