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.