Just went off roading on a new road but it was covered with jagged rocks. The Samurai took the terrain pretty hard, is there something that can damper the roughness? or is this just natural with most Samurais' and I shouldn't worry about it hurting the 4x4? 

Did you try lowering the air pressure in the tires

I was at 15psi on the colorado run (one of the trails) and it was nowhere close to what it needed. I had a rough ride as well, but attributed that to the short wheel base on the Samurai. The other guys said that if I would have went lower yet it would have smoothed it out more. Next trip i will drop them to around 8 to 10 psi. I run 32x11.5x15 Pro Comp Mud terrains. I would play with your tire pressure until it smooths out somewhat ( but remember its never gonna be like driving on the street).

If you have old shocks then you should go get a new set, the cheapest you can find.  Otherwise they tend to be to stiff.

On stock Samurai's we used to cut the bump stops in half or more to give the suspension more travel. Stock travel is only around 2 inches.

              Ed