OK, well firstly on what you've said I would do a full knee re-assessment to check for any other structures injured. Just to rule out any other cause.

The bilat squat need to be better quality. If he can only bilat squat to mid range with correct biomechanics and full weight on both legs evenly I would stop there. When he is going down further his biomechanics and technique will suffer due to compensation.

My initial suggestions are taht you need to also assess the hip and the ankle as they play a vital role in knee stability.