Pain on pinky toe joint from cleat setup?
Assuming that your shoes are wide enough and your front strap is not too tight, try moving your cleat sideways towards the crank arm. 

This will move your foot out a little towards the outside of the pedal and reduce outward pressure. It worked for me when I had a similar problem. 

Also make sure that cleats are not too far forward. They should usually be positioned so that the pedal axle is under or slightly behind the ball of your foot.