Longer shackles only move one end of the spring. On a factory SWB Jeep the shackle end is opposite the pinion side of both axles. So, by dropping that end of the spring down with longer shackles, you are rotating the pinion upwards. It can actually help with the vibes.....you just don't want to rotate the pinion too far, so you may need to remove or change any shims you may have installed with the suspension lift.
There are also issues with steering and spring fatigue that can come up, but with your 4" springs, you would be fine with up to a 1" shackle.