ouch. Did your PT and Doc check the footbed-boot interface?
They looked at me on just the Superfeet on the floor, then in my standard Nike cross-training shoes, and in my hiking boots, and in all cases, my knees lined up better with the Superfeet than without. They said I was "lucky" because I "didn't require custom orthotics." The proof is in the hiking though because I've been "cured" now for 18+ months. They worked for me (along with some other things, of course, but certainly they took care of pronating.)
You should see my old hiking boots - the lateral (out) side of the sole is worn down WAY more than the medial (in) side. My new boots are wearing perfectly evenly.
Tim