You're probably on the right track. Aches like this (and the neck soreness) can be a sign that you're pushing harder than your body is ready to go. Try slowing down a little, and relaxing, top to bottom, while you run.  Other possibilities include overstriding (reaching out with your front foot for a longer stride and landing with your knee locked) and wrong or worn out shoes.

Len

You might try adding some foam roller exercise if it continues. Also add strengthening exercise like using toes to grag a towel or marbels off the floor. Use a broom handle and place it against your instep, use it to add resistance as you flex your foot upward.

Best,

Personal Trainer Hollywood - Studio City