I had similar problems which were cured when I got new shoes. I could ride 75 miles and the next day couldn't go up and down steps. I bought Specialized BG shoes and I'm now pain free. As I understand it, feet are either varus or vulgus with 85% of people being varus. This pertains to the angle of your foot when hanging free. Sit on the end of a table with your feet dangling and you'll see that your big toe is probably higher than your little toe. The BG shoes have a small built in wedge that supports the foot so the knee is properly aligned. Go to Barnes & Noble and browse through Dr. Andy Pritkin's book, Complete Medical Guide for Cyclists. You can also go on the Specialized site or just Google varus foot.

You don't have to buy new shoes. You can get varus inserts that do the same thing. It really worked for me.