Any chance you can provide some video footage of you squatting? It would provide mountains of diagnostic information.

Also, you’re describing some pretty heavy mobility descriptions in your first post. Chances are that you have an absolute minefield of tissue problems all around that knee that are just flat out making that squat feel brutal. 

One thing that is important to understand is that none of these mobility interventions are overnight solutions. Often, they can provide some great on-the-spot relief, but making true change takes consistency and intent. Think about it like this: you’ve been out of exercise for a long time. Your body is a wicked-awesome adaptive machine, and it has spent that entire time adapting your body to a sedentary lifestyle and to whatever poor movement habits that cultivated in you. It has been adapting to that stimulus for… years, I presume? Now you’re trying to make adaptations in the opposite direction. It may take quite a while to turn the ship around and get your body back into pain-free,supple, ninja-like status. It might not take as long, as the stimulus of intensive mobility work and exercise is a little more aggressive, but it does take a lot of consistent work and deliberate action.

This is not meant in any way to discourage you, but to prepare you for the road ahead. It’s a big journey, but you’ve already taken the first few steps, and you’ll feel more awesome with each new mile you put behind you.

Now, regarding your particular issue, the big red flag here for me is that you’ve only got a 45deg active straight leg raise (and that’s me assuming that you’re performing that with strict standards). This indicates that you are missing a considerable amount of fundamental hip range of motion and/or spine stability. All major lower body movements are going to depend on the basic qualities expressed in the ASLR. You’ve already begun working to open up your hamstrings (this will be a battle, that’s some heavy-duty meat), but you did not mention any mobility work for the quads, and I think getting after the front of the thigh is going to be important here. Your hamstrings and quads work in concert to create and control the movement of the knee, and problems in one or both of these groups can cause that knee to articulate in a not-so-hot fashion (grinding and pain, perhaps). Get on a foam roller, beg the Mother for mercy, and deal with some of that quad stiffness.

Also worth exploring are your adductors (inside of the thigh). Speaking personally, adductor stiffness always causes inside knee pain along the joint line in my previously-injured knee, and I’ve noticed the same with several other individuals. Some of the muscles here travel far down the femur or even cross the knee, so tension here can be a significant problem. It would make sense for them to cause problems when squatting as well, since they are loaded when you push your knees out.

If you can summon some video footage, we might be able to tell you more, and with more certainty. Good luck.