Another simple solution to problems like this is to go clipless and stiff-soled cycling shoes, like Sidi Dominator, and pedal with a level foot, getting much of the pedal force through the shoe's heel cup. My cycling shoes are so tight in the toe it's hard to walk far in them, but on the bike they are extremely comfortable on 200+ mile day rides. Some of that is just the clipless setup, but some is also a bike fit that allows comfortable pedaling.
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