When replacing the shackles on our 93 YJ I found that after removing the nut and bolt you need to remove the metal bushing in the middle of the rubber bushings before you try to remove the rubber bushings. I used a punch and hammer to remove the metal bushing.
On the rear, I could not remove the bolt (gas tank in the way) until the rubber bushing was removed. To do this I first removed the spring end of the shackle. Then I removed the nut from the top of the shackle and the outside half of the shackle. Then I used a punch to push the bolt through far enough so that I could also push the metal bushing through. Next I removed the outside half of the rubber bushing with a pair of pliers. Then used the punch to force out the gas tank half of the rubber bushing. With the bushing out there was enough room to wiggle the bolt free without cutting it.
Overall, this was a pretty easy job.
2000 Jeep Grand Cherokee V8 Stock
93 YJ I6 hard top (really belongs to SPEED)
RE 4.5" Extreme Duty Lift, Advanced Adapters SYE, Tom Woods CV Drive Shaft, EA589 10" rims with 33" x 12.5" MT/Rs
Bullet Proof Front and Rear Bumpers and Tow bar