When I ride over 4 hours or so, I'll get something like this in my right foot, large toe. Been trying to figure it out for a while and then I came up with this answer; I'm using Speedplay Frogs on my road bike. They have tons of float. But what I realized was that my natural pedal stroke has my right foot rotating outwards a touch. That means that I get to the end of the float, and the shoe stops rotating, putting pressure on the opposite side of the shoe, right where my big toe is.
I just did a century. I made sure to be aware of the way I pedal and not let my foot move so far over. By the end of the day, I had much less toe pain than normal for that long of a ride.
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