TMonk I agree and think glutes are key. I was going to post something when you first talked about knee pain. As cyclists, we are quad centric. The quad gets stronger and shorter and pulls the kneecap out of place. The challenge is making a PT program operational. Not so easy. It is not just glute strength but neurology. The glutes just do not fire quite right. That may sound weir but it is happens.
My suggestion is to think about some glute / ham work with the quad isolated or being used for stability only. Bridges and Roman chair work come to to mind. Deads and back lifts and etc are great but I think glute focus will give a better yield (assuming we have the diagnosis right). Hey I stayed at a Holiday Express so what more do you want. For a combo exercise that use the glute and quad, try the one leg pistol squat and Bulgarian Split squats. I like the pistol squats. They kill my glutes. At my gym, we have a couple of good glute machines that I use.
There is no downside in making the glutes stronger and firing more during the pedal stroke.