So is your main question about your soreness? Sounds like it's just a flexibility issue. Trying stretching out in the off days and don't squat deeper than you can control the weight. Don't get me wrong, I think squatting A2G is great (and I do it too!) but if you lose control of the weight and you're just stretching/tearing the crap out of your muscles then it's not going to benefit you.

Do NOT worry about your knees going ahead of your toes. That is complete BS if you ask me. DO worry about your knees not bowing in or outwards too much. This can cause problems.

I'm thinking you maybe are limiting your knee range of motion and having to make it up in the hips and this is why you're getting so sore. Soreness from squats is normal (especially the first few times or if your volume is high) but it should not be painful. There is a fine line between soreness and muscle/tendon tears/strains.

IW

IW