Was this sudden or has it just built up over time? In my case I needed to loosen up the outer section of quad and work on getting the VMO to pull more, also needed to get more hamstring flexibility and strength. I had some PT, and did a ton of foam rolling, stretching, and various step up type exercises. I had similar symptoms of soreness after lifting, but you have to keep in mind there are so many other possibilities that may be aggravated by continuing work. If you're having x-rays done, see if they can get one looking down on your kneecaps with your knees slightly bent. In my case this is what showed the kneecaps rotated outwards from where they should have been. I went to two different places, the first one took a limited amount of x-rays, the doctor told me I should never do squats, lunges or anything (recommended wall sits) and prescribed me an anti-inflammatory and muscle relaxers. The 2nd one took about 3x the x-rays, really took their time, and actually figured out what was going on. It can be tricky, but if you can get any recommendations it can go a long way to finding a good ortho. I emailed a local crossfit place (because those guys have to be getting hurt constantly), and they recommended a PT place, and they recommended the ortho. You need to find one that specializes in getting people back to being active, rather than just keeping old people pieced together enough to exist.