The necessity of analyzing your lifts' range of motion

First off, I injured my right knee a year ago. Then I made some crazy resolution to pause squat every workout. I made consistent strength gains in my pause squat moving up five pounds a week which was what I expected because more so than any muscle group the leg  muscles are the most adaptable muscles on the human body and respond the best to training stimuli. This means you can make consistent strength gains all the time with any lift that uses the legs as the primary movers.

However, my problem with doing pause squats every workout is that it aggravates my knee injury and my right knee starts popping when I come out of the hole and my knee joint looks out of position like it's going to snap while I squat back up to the top.

My theory for why this happens is that in the squat the legs and feet are constantly fighting each other because they are in a fixed position on the floor, and they are playing a balancing act to find the best position to enable you to power the bar up to lockout. If that means the knee joints are going to take awkward positions to complete the lift because the legs want to complete the lift then so be it.

To remedy this, I've been doing pistol squats on a hack squat machine. This takes the legs out of the struggle of fighting each other and putting the knees into compromised positions because I'm only using one leg to make the lift. But the problem with this is since I'm using a lighter weight by using only one leg , I'm neglecting the torso and upper back muscles that are equally crucial to squatting.

Enter the good morning. It  taxes the exact same upper back and torso muscles that the squat uses. My theory is that the good morning coupled with the pistol squat for each leg will be a suitable substitute for the pause squat. Consequently I should be able to pause squat on one workout day and then do pistol squats and good mornings on the next workout day.  This should solve my knee pain problem and translate to strength gains in my pause squat.  My ultimate goal for the pistol squat is to eventually use no hack squat machine and move to using a barbell doing either back or front pistol squats.