Hyde
Legend
What I've found to be the case with myself and my training partners is that knee pain manifests itself when the knees come forward in the squat. Any time the knees come forward, there are tremendous shear forces on the knee joint. To help with the knee pain, you're going to want to keep as vertical of shins as possible. We accomplish this by, as has been said, forcing the knees out.
A simple "knees out" cue often doesn't do the trick, though. What works for me is "screw your feet into the floor". For others, it's "spread the floor". And sitting back a little more will also help you to both stay on your heels AND keep a little more vertical shin. Your quad involvement will be lessened to some degree, but that'll ramp back up as your depth increases and the weight moved goes up.
As you're not looking to compete in powerlifting anytime soon (I think?), there's no real need to push depth, just take what you get. You might be humbled at first if your hips can't take the load, but I've found that the hips increase in strength very rapidly, so you'll soon be moving much more weight than before.
I second everything here. Especially about the hips getting used to the weight quickly. Tough at first, but you'll get the weight back fast.
And I squat/pull in chucks. Changed my life.