You obviously have tight arches, which may be developing into a condition called plantar fasciitis. There is a thick band of tissue on the bottom of your foot from your heel to the ball of your foot called the plantar fascii. If it gets inflamed or irritated, it is referred to as plantar fasciitis.
Anyway, the best treatment for this and keep training is to change your mechanics like already discussed and doing several stretches, both before and after activity. You can take a towel, hold one end in each hand, loop it around your toes and pull towards you. The tennis ball idea is very good to do in addition to towel stretch. A variation of this is to use a golf ball to further pinpoint smaller tight areas. You can even put the golf ball in the freezer so it gets cold, the cold will help with inflammation as well as be a pain reliever.
It would not hurt to do the stretches / ball rolls several times a day to really loosen up the structures in the arch of your foot.
Good luck!