Looks good overall. You're blessed with great hip/ankle mobility, which puts you at a huge advantage.
I would personally aim for move movement at the hip and less at the knee, but there are many interpretations there. I would lean more toward the Rippetoe approach (not just the head position, but hip dominance). It would involve squatting lighter at first to learn a new movement though.
As far the hip shift/favoring leg, are you doing much unilateral work? split squats, reverse lunges, step ups, step downs, pallof presses? In simple terms, its hard to favor one side when only the other is working! I find a lot of people I train to have lateral imbalances, and its very easy to reinforce these imbalances when every exercise we do is bi-lateral.