Another thought, and I must say I AM SO NOT AN EXPERT. I have horrible achilles tendon issues brought on from backpacking and getting older and favoring a bad knee. I have changed my pedals to Shimano A530 platforms. On a long ride I will often clip out, flip my pedal over and ride a ways unclipped to allow my feet and knees the opportunity to move around. Another suggestion is to trade out your pedals to a platform, do some riding and see if that helps. Perhaps even going so far as to chalk the bottom of your shoe, go for a ride and see where the natural position is for your right foot. I know that sounds a bit corny but I totally get the frustrations of not feeling right on the bike.