you can seek help from
www.runnersworld.com , and they have some info on leg length and flat foot. Or maybe you can get help from their forum as well.
I do have some knee problems from time to time, and i would just put an ice pack on it before i sleep and let it stay on for the whole night. It does help.
Furthermore, you can do knee bends before you run, and refrain from running too much too soon. Always build up from the base.