+1 on the superfeet as a short term solution.
The typical pattern I see with this type of issue is weak intrinsic muscles of the foot (small muscles in the foot that help to support the arch), tight calves which create increased load on the ball of the foot, weak hip extensor, abductors and external rotators (weakness here messes with the alignment and loading through the leg, causing uneven loading through the foot.
I don't have any time to post links to exercises right now. I might get to that later.
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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