Shoot another video of your squats and such and if I see anything I'll tell you. But with the knee thing it honestly could be the loading. It is VERY possible to get stronger in terms of neural adaptations and muscular adaptations before your joints can catch up. The the closer you get to the joint the slower the strengthening of that soft tissue.
So, quite simply, you may want to just spend a few weeks adding reps or something, if comfort allows, while the knee strengthens. But it could be some technique thing that needs tweaking. Before everything looked pretty good to me though, squat wise.
The only other consideration is just not having enough posterior chain work. A big limitation of the "meat and potatoes" approach. One of the keys to knee health is hamstring and glute strength. Although your deadlifting the majority of your work is "knee dominant" as opposed to hip domanant. The single leg stuff helps A LOT but you may have to think about putting in some extra (light) pc work. Pullthroughs or romanians is what I'd recommend to start.
As far as the shoulders that is a whole big can of worms and there is not a simple answer for it.
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