Shaf, a couple of things...
First, if you close you eyes and just listen to the lifts, you make a lot of foot noise. Maybe not a huge issue, but I learned to use the least amount of foot movement I could possible have...this was a good hint from Stephan. Your feet also move between reps and that simply tells me that maybe you need to only do ONE kind of squatting for a while.
I'm not sure about the left knee. I think it takes about two years plus to regain the "courage" to trust an injury. Something as simple as using those bands around your knee (the thing the Westies do) to make you pull the knees apart might help in the short run.
So, one stance...maybe one squat. Certainly, Zerchers should be done...maybe just with heavy dumbbells (I call them Goblet Squats when done with dumbells because it looks like you are holding the Holy Grail)...between sets of squats. It's funny, but I sense a confidence issue here...and I have nothing but intuition guiding me on this feeling.
I would also add that when you get "caught" between disciplines...O lifting squats versus a "powerlifting" squat...I think your body also gets confused. That's what I discovered with Deadstop Front Squats. All it really did with me was teach me that I had to fire my legs out of the bottom and not just bounce. So, when I watch you lift, there looks like you have a gear change...and your left knee either tries to help or get out of the way.
So, one stance. Goblet squats...maybe some light fast ones, too, to groove the movement. Maybe the Westie idea of using bands around both knees. Certainly, you need to restructure you max lifts to reflect a year or so "not going so heavy." I found that 50-60% of old bests gave me a lot of work to realign the old pathways. Perhaps you can do the big quarter ton squat...but not every week now.