I recently had my yearly physical with the department doctor (city FD) and I mentioned to him about a lingering knee issue I've had for the last 9 months or so. He looked at my knee, turned it a bunch of different ways, put his hand over my knee cap and felt the grinding shards of glass inside lol-- anyway, he told me I had the same thing: patellofemoral pain syndrome. I asked him where it came from, he simply said using it and being athletic
I've done quite a bit of reading on it and have been spending the last several months trying to find a pain free way to squat. I love doing squats and I'm only 29 y/o. This is what I've been doing...
-Working on flexibility and mobility like mad. After every training session I stretch every single muscle from my low back to my ankles. This has helped greatly, pulling a lot of the stress off the knee cap. Some really keys stretches that work for me are:
a) Rectus Femoris Stretch
b) Garland pose (yoga), also focus on keeping your thoracic spine upright and straight and try to avoid "butt wink"
c) stretch the piriformis really well
d) foam roll the shit out of your quads, IT band, glutes. Focusing on the quads largely has helped.
e) ankle flexibilty stretches
Do that stuff and before every single squat session I do...
a)leg swings, warming up the hip, front to back and side to side
b)Garland pose, a few times actually
c)strechting the rectus femoris very well
d) 2 x 10 overhead squats with a broom stick utilizing a true snatch grip (bar across your hip crease when standing)
e) easing into my working sets very slowly, starting with just the barbell
d)EFS Heavy Knee sleeves (NOT the super heavy)
This has helped me greatly, and I've started doing front squats trying to build my quad strength back up as my hips were dominating for so long from low bar squats. I just have to mindlfully focus on the mechanics more when squatting with every rep. I went from not squatting anything for a few months to front squatting a decent amount of weight again. Hope this helps, best of luck.