A nice trio: exercises for core, back and leg strength

I've been experiencing annoying nagging soreness and swelling in my knees thanks to to doing reflexive squats and then alternating with pause squats.  The range of motion in both exercise forms is identical so I pretty much expected pain in the knees. The problem is for the strength gains to keep coming in the squat, the range of motion where you bend the knees and lower the glutes to almost touching the ground  has to be severely taxed and stimulated in a consistent manner.  So how do you make strength gains in the squat with limited knee pain?

Enter the acute angle deadlift. The beginning of the lift has you standing  on two stacks of two forty five lb plates stacked on top of each other. One foot goes on one stack. The other foot goes on the other stack. The stack of plates on either side of the barbell remain on the ground. This forces your body to be in a balled up position. Your knees are in a bent position but not as severely as in the squat. Your lower back and shoulders are in a rounded position. This places a great amount of stress on the legs and lower back so quit when you start to experience severe soreness in the lower back.

My theory is that the combination of alternating  the pause squat on one workout day with the acute angle deadlift on the next workout day will see an increase in the reflexive squat with reduced knee soreness. I say reduced because you'll always experience knee soreness if you bottom out while doing squats. Another benefit is if you make a strength gain in the acute angle deadlift it will transfer to a strength gain in the deadlift. Also if you make a gain in the pause squat I'm theorizing that a strength gain will be made in the acute angle deadlift.