Pain on the 5th Metatarcel and Cuboid
With these shoes you probably use Shimano's SPD-pedals or similar MTB pedals. Most, if not all of these do have some angular float of the heel when the clip is engaged. It is part of the system. I'd worry if there's no float.
As with the pain on your left foot it could be caused by the position of the foot on the pedal. Ideally the axle of the pedal would be under the ball of the big toe. You might experiment here by moving the cleat fore or aft. Go for a ride, take along an Allen key and experiment settings.