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...I've had similar issues that limited my rides to 20 miles or less for about the past year.
A combination of (non-prescription) orthotics from an online supplier of these
along with MKS AR-2 road pedals (wider and low profile) and some stretching and custom forming of some Shimano SPD shoes worked for me.
But it took me over a year to figure it out. Anything at all in the cleat position on the shoes (even just the blank rubber plate that comes with the shoes) seems to irritate whatever it is. And I take off some of the sole every now and then with an angle grinder to level it when it wears down on the outside.