@roman1982 This is one of the best overall transformations I've seen on here, as you noted, great
overall progress. Especially the delt/lat area. But don't sleep on your calf development, that's a very noticeable difference. Quads look great as well. Those two together (but mostly calves IMO) really changed your physique to look more aesthetic and athletic.
On the squat front, it took me about a year to unfuck my squat after similar lower back and knee issues. In my case, from low bar squatting and chasing numbers (weight on the bar). I switched to a high bar, knees forward, upright position and really slowly progressed the weights using reverse pyramid training as a way to focus more on reps than weight. Andy Baker's upper/lower program from his website is what I followed. Coincidentally I also wanted to do more calisthenics so I replaced a lot of the assistance work with bodyweight stuff.
But again, great work. Very motivational, thanks for sharing.