Yup on the reason for the rough ride. Most forget to reposition the shock mounting points when they move the axle from below to above the spring resulting in the shocks being mounted wrong and no longer being in the "sweet spot" in normal driving.... If the shock mount is repositioned to maintain the correct length from top to bottom mounting point the ride will remain the same.

BTW, Speedway Motors sells a pair of 3 position shock mounts for the rear end housing for about 10 bucks a pair.... Work great, have them on my '71 pickup.