Funny thing: I have a '91 YJ and installed a 2.5" RE lift last June. At first I was happy as the ride initially felt a little smoother, but for the last few months has been literally bone-jarring. I did look for some advice that suggested loosening up the shackles a bit to 70-80 ft-lbs. Didn't do too much.
On my YJ it was always the rear that felt like it was kicking me in the arse, so last night I installed a new set of 3/8" lift greasable shackles in the rear and so far the ride seems way better. Could be a combination of the longer shackle letting the spring get longer as it compresses, and the grease in the bushing.
A side benefit of the lift shackes is that the rear had sagged a little, and now it sits just right. Anyway, so far I couldn't be happier with the ride. I'm heading on a road trip tonite in the Jeep, so I can confirm if the ride is really that much better for you tomorrow.