Off the top of my head:

* Front drivetrain (hubs, half shafts, diff, mounts, drive shaft)
* Transfer case (different crossmember?)
* Rear drive shaft
* Center console around shifter

Like you said, you could then swap in either the longer '99 4WD V6 coils all around, or go for some aftermarket lift coils. If you have your heart set on keeping your current 4Runner, maybe start looking around for a totalled '98-'99 4WD auto model that is cosmetically beyond repair, but has an intact drivetrain. Of course the mechanicals from pretty much any '96 - '02 4Runner will work, but the later the model, the greater chance you'll have incompatability issues with ABS, traction control (TRAC), skid control (VSC), and multi-channel brake layouts.

Can it be done? Sure. But I'd look at ALL the costs involved before ruling out a trade or simply selling yours and finding one with the equipment level you want. While we all enjoy our 4Runners, they are not classic cars, and as such, make a poor choice for dumping tons of money into.
The other point you want to consider is that it may be harder for you to eventually sell your current, modified, 4Runner. Buyers may not be as keen on the 4WD transplant as you are.

Andreas