Knee Pain and footbeds

Last Saturday (25th) whilst out riding I began to get soreness in both knees, when climbing in saddle. This developed into a slight pulling down the front of my calf and aching within my knee. I did a quick and easy 10 miles on Sunday hoping it would go away. Had Monday off and then did chain gang on Tuesday, although I kept up I had lots of pain in my knee's. Stupidly (probably) I then did 35 miles on my MTB on wed as I was planning to race in wales this weekend. Thursday when to the doctor who told me to stop riding for a week, which so far I have managed and my knees seem much better.

I normally spend a lot of time out of the saddle and it's already been suggested to me that I should try pedaling smaller gears and sit down more.

My other thought was to try using foot beds. I use Specialized shoes so it would those that I would use, my LBS stocks them but as yet I haven't been up there to talk to them about. Anybody have any experiance with knee pain or the foot beds? Thanks.