I am not a lifting expert by any means, keep that in mind... but I can tell you for sure that you should never decrease depth to above parallel... it will put too much stress on your knees and also will prevent strengthening so much of the supporting cast muscles necessary for true development of squat strength.
Lower the weight, focus on form (feet planted shoulder width, 30 degree angle, CHEST UP AND OUT throughout the entire squat motion, drive up from your hips not your feet), and focus on strengthening your core with a lot of core exercises after your workouts.
takes time, but it will be worth it. It is a process I am going through myself.