Typically you need a little heavier % weight to check for knee valgus. Mine isn't noticable until I get to 500lbs+.
I 2nd getting rid of the box. Personally, I think they're really only good for noobs or geared lifters. Regular pause squats are superior for a raw lifter IMO. I personally have never done box squats and even with my shitty build for squats I've been almost to 600lbs in wraps before and can hit 500+ in sleeves basically any day.
How do you descend? Do you just kind of drop down and try to stay balanced? Or do you root your feet into the ground, fill your belly with air, lock in your lats and then pull your chest into your knees while opening up your taint and keeping your knees tracking over your toes and your neck driven back into the bar?