you've got a lot of info to digest there so I don't want to overload you but there is a bone simple flexibility drill I have used and continue to for the squat, warming up or cooling down etc. (this may even be on Bob's squarrx vids..I don't know)
The first is what I call a stripper squat. Find a pole or post that you can hold onto at about belly button height standing about 3/4 arms lenght away. you could also use a sturdy doorknob
hold onto the pole and squat all the way down ( the proverbial ass to grass that few ever actually hit) using the pole for balance. you can really lean back, round your back and settle into a deep squat. with your weight biased to the heels. it sound kind of silly but by using a little assistance you can work up to sets of 20 to 30 very quickly.
once you're comfortable with it you can use this stretch to hit all the squatting infrastructure just by leaning one way or the other and widening or narrowing your stance, or just focusing on pushing your knees apart. at the bottom let your back round and then practice moving into a solid arched position with chest up shoulder blade pinched and then back to an exaggerated relaxed round back. if you know any yoga stuff I think it's like a "squatting cat/camel" if that makes sense.
it sounds like a simple thing but i used this movement to rehab from double patella relocations. I went from chronic pain and a limp three years ago to being able to squat heavy-ish twice a week now without pain, regardless of how tight my hams are, I never lose my arch. If I develop hip flexibility issues or have trouble hitting depth on a heavy squat, I'll crank out several hundred of these throughout the day for a week and it really loosens up. Sorry if this is a bit remedial, but it really helped me..