What brand of shocks did you have installed?
Are the insulators and washers properly installed on both sides of the shock-to-frame mount points?
Can you reproduce it by pushing on the rear quarter panels up and down or side to side?
If it happens more when the left and right suspension are at different lengths of travel, I'd look into the sway bar end links and axle insulators. Maybe even the watts link and control arms. But since it really started with the replacement of your shocks, I'd focus on them.