Pigeon Toed Squats?

When I was a kid, I had to wear leg braces during the day, and shoes with a metal bar that forced my feet outwards in bed at night to help "cure" my pigeon toedness. These were not pleasant contraptions and ultimately made zero improvement. My parents eventually took me to see an orthopedic surgeon for x-rays and to see if there was a surgical remedy, and there was: to cut the femur and reposition my legs, because my hips were turned so far inward. Thank GOD my parents passed on that option!

Fortunately, my condition never really bothered me - and thankfully, I wasn't teased much about the braces either. As an adult, my condition turned out to be a benefit for martial arts, helping with my turning round and swing kicks.
Today I ran into an exercise that brought the condition back on the radar for me: Overhead Squats. These were really tough! I was all over the place - my right knee wanted to move inwards, and my right heel wanted to lift off the ground when I had toes out. Or I'd lose my balance. Of course the upper body and core work was challenging too.
Could the fact that my hips are turned in more so than most people mean that I need to have a modified foot position? I'm still not sure.
Jeff suggested this notion long ago. It would make sense that the muscles and ligaments connect in such a way that pointing my toes out would twist them into an unnatural position.

After the workout Mike and I looked at some different foot positions for me, and one issue is my knees weren't tracking over my toes. When I did this, there was a marked improvement. Also, when I tried to keep my upper body perpendicular to the ground I'd fall off balance. Leaning forward (but still keeping the lumbar curve). I also recognize that my muscles are just not accustomed to this type of skill, so there are certainly flexibility and muscle weakness issues at play too. I did find an interesting thread in the CrossFit Discussion Boards about Toe Positioning For Squats.

WOD
Five rounds for time (35:02 - this is by far my longest workout! I was tired today....)
95 pound Snatch, 3 reps (I did baby bar)
95 pound Overhead squat, 15 reps (baby bar)
Run 400 meters