Experiment with stance more, drop the weight for a bit, and keep playing around with your footing until you REALLY find the position that works best for you. Sometimes a slight change to stance width and foot angle can make a really big difference, and some people never experiment enough to ever really find their optimal groove because they settle into sub-par positioning and keep with it.
The wider the stance, the more important it is to angle feet outward, push the knees out, and learn to use your hips (squatting wide powerlifting style is almost nothing like a normal bodybuilding squat). Narrower stances are better for many people with feet only slightly angled, as too much flaring outward can shift things and cause knees to cave in. I've seen a LOT worse than what you have going on, I think that with more experimentation, you'll figure things out in due time.
But, definitely do not skip the assistance work, be sure to roll out your quads/hams/hips before squatting, and trying things like paused bottom squats, partials, rock-bottom squats, etc will all help in their own way, but first things first, I'd suggest really working on your stance to find what's 100% most comfortable and you'll likely see some improvement as you build on it.
I had a personal trainer at my gym tell me i'm going to have a lower lumbar injury if I'm going to keep squatting the way I do. Consequently, he has never powerlifted before and said that my "hip drive" was improper. Don't let some people who have taken an online course or a couple classes tell you your form is ugly or what not.