Are you still on your LP? How old are you? What have you done to work on fixing your knee pain?
I, just a guy on the internet, don't think your depth is a problem. Wait for the expert opinion on that. What I do see is that you're lifting your heels at the bottom of the squat. To me, it looks like you are getting over your toes and your knees are sliding forward after the point in the descent when they should be set. You know you need to point your nipples to the floor, so the next thing to aim for is having the bar over your mid foot at the bottom of the squat, not getting over your toes. Try getting your knees set earlier, like 1/3 to 1/2 down and sitting back more. Also you need to work harder to keep your knees out. Toes should be pointed out about 30-35 degrees and your thighs stay parallel to your feet. At your next workout, try filming with the camera a little higher and maybe once directly from the side to observe the bar path.