I used to work as a Master Tech at a Toyota dealer, and various independents, and still have friends in that line of work. There are lots of 3rd gen 4Runners still running around, the newest of which is now 17 years old, like yours. If they have the stock springs, those springs have inevitably sagged leaving little suspension travel, with a corresponding rough ride, regardless of the shocks used.
For the softest ride, I'd suggest new OEM springs and shocks. And also use OEM speced P-rated highway tread tires.
KYB Gas-a-just have much firmer damping than stock. And the KYB Monomax are much firmer than the Gas-a-just shocks.
Also if you haven't replaced the lower ball joints, I would do so soon with OEM only. Aftermarket LBJ's simply aren't made as well. And since the design of the LBJ's on 3rd gens isn't the best, failure can be sudden and catastrophic.