I agree with Knott. this is almost certainly a metatarsal arch issue and could be handled with the right insoles. Just make sure you're getting a pair with the metatarsal arch pad, or add one as Knott suggested.
It is also a good idea to move the cleat back a bit. Try lining up the axel of the pedal with the joint at the base of your baby toe.
Knott, thanks for posting about the Berry. I haven't seen them yet but I'll definitely look them up.
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2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS