Josh... For a start... - make sure your knees do not fall inwards on the power stroke. The general approach is that it make you more aerodynamic if you have your knees close to the frame, but it will place huge loads on your knee. Make sure your knee "follows" the foot - i.e. you should be able to "see" the space between the 2nd and middle toe on the inside of your knee as you cycle. This will sort out the load at the knees. - spin slow - stretch your ITBs. This may sound strange, but the ITB has attachments to the knee cap that pulls it out of alignment which aggrevates the runner's knees. - strengthen you bum Try these, it should help. Let me know if you want more specifics For the collapsed arch, it could have many causes, so not so easy to give advise Good luck