A lot of the rough ride comes from the rubber "overload" springs in the rear (rubber cones inside the coil springs).

Once they start making contact, the ride really gets nasty.. and the rear springs on 4Runners have a habit of settling with age, making more contact.

I use Monroe air shocks on the rear to partially overcome permanent added weight due to various mods, and the lift the back end up a bit..

The ride when the shocks are pumped up to 100psi improves significantly.. I'm sure no doubt to keeping the axle from hitting the rubber cones inside the rear springs...

The other thing that causes a rough ride is the front anti-sway bar is very stiff.. and when you hit a bump that wants the rock the vehicle side ways, the stiff sway bar snaps it right back..

I presume they did this to make the vehicle as roll over proof as possible on the highway.. For this reason I haven't touched mine, but sure would like an easy in-cab disconnect when off road..

Take a quick look at the diameter of the front sway bar and you'll see what I mean..