From what I have picked up on this forum:
Lift springs - the more lift, the harsher the ride.
Spring quality - cheaper is not better riding. Old Man Emu or Rubicon Express are the better ones from what I have gathered.
OEM style oil filled shocks only, no gas charged shocks. The oil-filled just dampen the springs. The gas charged expand themselves when unloaded, so now you have to compress the spring AND the shock...
Tire pressures overinflated - just because the sidewall says 50PSI doesn't mean that is what you run them at. That is the pressure for the max load the tires are rated for. Search on here for tire pressure recommendations to figure out what is best for you.
Also check spring bushings, as if the shackles were overtightened then the bushings cannot flex as designed.
Hope this helps...
Oh, an afterthought - CJ5 means you have a short wheelbase. This amplifies the roughness. The longer the wheelbase, the smoother the ride.