Hi, PG
Both saddle height and saddle fore/aft position can affect your knees. Assuming your saddle is in the right height, the next thing is to look at your foot position. I learned it the hard way!
My bike has been fitted by a very knowledgeable bike shop guy, but I ran into sore knees after getting a new pair of shoes. It wasn't until well after th 100km organized ride (after which my knees were agony) that I checked the cleat position on my shoes. You want to ensure that the ball of your foot is lined up with the axel of the pedal. If you have SPDs make sure that your cleat is positioned so that the ball of your foot is in the right place.
Sending butterflies to help you find pain-free riding,
~T~



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