Nice sessions going on in here. Is your knee pain just below the kneecap? The patellar tendon? I suffered patellar tendinosis for a loong time, and what actually did help it was trying to exaggerate my knee spread.
Single leg work like Bulgarian split squats, lunges and stepups might be something to add into your training. They really build up the vastus medialis and will help with knee tracking, knee stability and hip stability. They suck, but sometimes a necessary evil!