Or your cleats are not properly adjusted over your axles, putting stress on weird parts of your foot/leg Even if you do not have cleats for your pedals, if your saddle aligns your legs with your pedal axle porrly, your knees may be stressed.

Try adjusting the fore/aft position of your saddle. Also, those Bontrager stock saddles are icky. I had major fit issues until I replaced it with a better saddle Apparently, I was not "perched" correctly on the saddle I was on (it was too wide) so I bought a Specialized Ariel and it increased my riding comfort immediately!

Still tweaking my fit but I didn't realize how much pain and suffering my saddle induced until it was switched out with a better one (i.e. one more suited to my physiology).

Your bike sounds great--you should post some photos so we can all drool over it and tell you how shiny and beautiful it is!