try beefing up your VMO first and see if that doesn't fix your knee pain problem. In most people the VMO is weak and thus causes the patella to not track properly causing pain.
The VMO atropy faster than the othe quad muscles when you layoff, so hense the lack of balance when you return to training. Also why when you start training, one should do stepups and split squats to strengthen the VMO before doing squats.
Doing box squats and PL squats will just amke the problem worst, since your VMO will just about shrink