Take a break from squatting for a few weeks (2-3) and really work on improving the flexibility in your calves, glutes, and hams. I had a couple knee surgeries and developed what they called patella infera and other patella problems, tis simple stretching Im referring to here helped tremendously. Problem is, squatting when the calves, hams, and glutes are too tight is gonna increase shearing forces in the knee joint AND inhibit the glutes from contributing to the exercise. Also, while working on stretching those muscles, work on strengthening/activating the tibialis anterior. I strongly believe this will help.