Erik, your squats look great man. I think based on how you squat you could really benefit from wearing Olympic weightlifting shoes with a heel on them. They will help you get a little deeper and I think you will notice an increase in force. However, these are not a necessity. You're doing great.
You have great posture under the bar. Knees, as far as I can tell, track well. You stay tight. You even have developed a little bit of a bounce out of the hole with your hips (which can be a good thing).
Don't worry about your shins not being upright. That is applicable for really, really wide stance squatters, usually powerlifters lifting in a squat suit. They are sitting into the suit and letting it drive them out of the hole. An entirely different application than what you are doing here as a raw lifter. Especially with the design of your body and limbs. Anatomically, it would be hard, if not impossible, to keep the bar over your mid foot/center of gravity with a medium to regular stance while maintaining perpendicular shins. Try it with a broomstick.
I think you are over analyzing your squats man. Awesome idea to post up and ask these questions, but I hope I can rest your mind and telling you that you're worrying about a lot of insignificant details. Keep lifting and getting stronger. You seem to be doing well.