are you getting alot of side to side motion through the pedal stroke? forefoot varus?
i added some shims to my cleats. my generic, all the time, sort of knee throbs seem to have gone away since i did that.
i also run and hike. its nice to get out of the 2d motions of the bike. cross training and stretching will probably help - but i'm no doc!
So long. Been nice knowing you BF.... to all the friends I've made here and in real life... its been great. But this place needs an enema.