Hope this doesn't sound too obvious... but loosen your shoes part way through the ride. Most people's feet swell a bit during a long ride (especially if it is hot), so a shoe that was comfortably snug at the beginning can be come a torture device by the end if you don't adjust it.
If its not that, think about different pedals - some pedals, especially those with small platforms (like SPDs) can cause problems, because the force isn't being spread on a wide enough area of your foot or they are irritating a nerve.



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