Sentoguy: I was doing the "Couch Stretch" (http://www.youtube.com/watch?v=-ZX1QMTdAC4 shows you at 2:30) and just the regular calf stretch (http://www.youtube.com/watch?v=e4cpBBDVGGU around 3:15) for 30 seconds at the beginning and 2 x :30 at the end. I did contract-relax on both. I definitely am more flexible on my left side now due to the stretching, but when I squat the problem is still there.
theBird: It is pretty bad if I don't think about it (which I have changed) if I just plop down I am pretty off my center. A fairly accurate example would be like this: http://www.tru-strength.com/wp-content/uploads/2012/07/Sheldon-105-kg-snatch-catch-LAS-961x500.jpg. My right hamstring is typically closer to my calf (I only go to parallel not ass-to-grass) and the external rotation of my left leg looks suspect compared to my right, judging from the knees over my feet.
alexus: I have never thought about imbalances in my set up... My hands definitely stay even on the bar, but I don't know if the bar stays even on me. I will check that out and let you know. As for the test, I checked it out and my left side can touch closer to my chest but my lumbar curve breaks more (squeezes to the ground more) even if I try not to! So hamstring/back thing maybe??
Thanks for the feedback, I appreciate the insight and help