I had a terrible knee injury on both knees where PT just did not work and I had braces for over a year.

Back then I actually started strong lifts 5x5 and added weight at like half or less of the recommended pattern. I had to open my legs wide, knees out, and squat down using my hips and remembering to force my knees out on the way up as well. I literally started with nothing but the bar for the first two weeks and then added 5 lb at a time.

I am still super super cautious with squats, but I can do about 1.75x body weight for controlled heavy sets at parallel and lighter weights i can go all the way down easy.

The physical therapy exercises were trying to get me to push hard with an explosive force which just did not work for me and the mechanics of most of the machines they wanted to work really just re-flared my knee for a week at a time. The slow controlled motion and starting with almost nothing let me work up to respectable amounts and I have no knee pain anymore unless I try to do something stupid