Were your shackles a total of 8" long? It looks like the ones in this picture are about 7" long
So that would make your old shackles give your Jeep about 2" of lift. I'm not sure if that would cause you to need new shocks or not, but if your shocks are becoming fully compressed, or your are hitting the bumpstops that would give you a rough ride.
One of you jump on the bumper, while the other crawls under the jeep and looks for any place where the suspension would be hitting. I'd think that it will either be your shocks or your bump stops.[addsig]