well your foot is weaker, this makes it so you cannot screw it into the ground optimally. Now, when you cannot create torque in your foot, your in a bad position and you cannot get your knees in a good position. This could be causing the little pain in the knee. To fix that you will need to work on your motor control. Now for your foot keep doing what your doing. DON’T GO TO FAST WITH BAREFOOT SHOES. They are great but take a progressive approach so you don’t get hurt doing to much to soon. Do these things and it should resolve.