I was using those things on my right shoe to correct the exact same problems you're talking about when my knee and foot problems started. I can't say they caused the issues because there were too many factors involved.
Based on where my foot pain was located my podiatrist thought I had 2neuromas. He was shocked when I had no pain when he manipulated the area. For awhile I used met pads on my orthotics but they caused more discomfort.
I used to wear shoes without heels. I read how they can cause foot pain. I quit wearing them, my foot pain went away. Since having my SI joint adjusted my chronic knee pain also disappeared.
At the time I also had a saddle that was too wide for me, not sure if that contributed to my issues or not.
I no longer wear custom orthotics, just Superfeet Berry in my cycling shoes and ski boots. This season, I'm hoping to not use them in the cycling shoes.
BTW, the wedges I had were installed between my Speedplay cleat and my shoe.



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