Well, I am basically just re-watching the videos that you sent me in the original post. The main issue is that I have consistent knee pain while squatting with an arch. It’s not any part of the quads, or any muscle related part of my knee. I have since bought orthotics for my shoes.  It’s a  moderate improvement, but any improvement seems like I just won the superbowl. There is no knee pain from any other movement. When I practice body weight squatting alot, I notice that I ahve alot of knee pain when i try to arch my foot in the way Kelly advocates. I am probably just post footage from now. This week I will do just that with a bar. 

You may be trying to push your knee too far to the outside of your foot, maybe even past your pinky toe. Keep the foot arched up, turn them out slightly, and just sit down, don’t think too hard about pushing the knees out and just let them fall in line with the feet an ankles and see what happens.