Have you watched the rebuilding your feet 3 part series?
Rebuilding Your Feet With Brian MacKenzie
Rebuilding The Feet, Part 2
Part 3 http://www.youtube.com/watch?v=4h8uxhXhozY&feature=player_embedded
Episode 349: What If We Just Used a Joint Stability/Function Approach?
MWOD Pro Episode #3 The Flat Feet Solution
Episode 343: Stop Walking Like the Duck You Aren’t
Go barefoot as much as possible.
Wearing vibrams asks alot more out of your ankle rom, achilles, hams, heel cords etc. Doing too much too fast can lead to a set back.
The pain in your knee could be caused by several different thing you would need to give more info on it.
For your squat go after the hip first. This is where you will see the biggest differences.
Your knee is downstream of the hip so this could be an impacting element to your knee pain.
You may be hyper mobile at the knee. This is addressed a bit differently.