Knee pain, hotspots on the foot, knees not tracking straight up and down through your pedal stroke - there is a solution. I didn't realize how easy the problem is to solve. The word for the day is footbed. I have never seen a "stock" footbed give the support needed.
I used a footbed with support in my previous pair of shoes. It took away the pain and made me more efficient. Recently I bought myself a pair of moldable shoes, and the footbed itself was moldable. Did I mold it? Yes. Was it comfortable and efficient? No.
After the fact, I bought myself a pair of footbeds, a pair that fully supports my arch. These footbeds took away my foot pain, helped my knees to track straight up and down, and relived some discomfort I was having with my knees. I have learned that it is better to buy a 100.00 pair of shoes and spend 40.00 for a footbed than to pay 300.00 for a pair of shoes and use the stock footbeds.