hey, simple simple question: what kind of pedals????
afterall, most pedals are lock-down cleats, like the spds, spdrs... unless you shucked out lots of $$$, you are not getting pedals with a good float, and that means locked knees for hours on end.
my patellas grew in incorrectly, i can't even jog for 5 min without falling down and crying, but i can bike, a lot. invest in speedplay pedals or look. as to numb feet, specialized wsd shoes are amazing slightly wider, slightly shorter than men's so there's no slipping when you get the right width, and no pinching for the right length