Surprisingly little has changed between 1996 and today with regards to suspension and chassis design used on the 4Runner. Some models of the newer 4Runner has the active XREAS suspension, which helps a little, but overall if you do a complete overhaul of the now 18+ year old suspension you'd be surprised how well a 3rd gen rides.
I just did the whole front end of my 275k mile 4runner, along with chipping away at the squeaks and rattles developed over the years and cutting down on road and wind noise as much as possible. Makes for a surprisingly smooth, comfortable and quiet daily when you consider that at the end of the day it's a worn out old 4x4.
Seats make a big difference as well. Basically all of the stock 3rd gen seats are completely shot by now, reforming and rebuilding the seats is starting to become more of a common repair and something I definitely recommend if you're trying to make it more drivable. Main complaint I have about my sister's 5th gen limited is actually the seats, they are absolutely terrible.
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