Well lets see, first you do need those pads, they are the only insulation between axle/road and the rest of the car. As far as the "poly type" my preference would be to use the original rubber type instead. They will definitely provide a better ride.
Changing them out may solve your problem, if it doesn't than you may have to fabricate some shims for the top or bottom of the spring pads. 5/8 of an inch really isn't that much in the grand scheme of things other than personal preference. Since you replaced all rear end suspension components, double check all your work, you may find the answer there as well.
