Have you tried box squats with a heavy emphasis on sitting back (keeping your shins perpendicular to the ground or even further back). If you find yourself plopping on the box I suggest raising the box height and working the height down rather than working the weight up.
I would be sure if it's possible to include at least some sort of squat variation just to keep the movement pattern grooved.
Can you squat your own bodyweight without knee pain? You might even want to do some really light form work with the bar if possible.