Ok, so 10 years after the creation of this thread, doesn't look like anyone has ever attempted to install the VF4 t-case into a 5th gen that originally had the VF2A t-case. I started researching this topic as I'd like to add a 5th gen to the stable, but wanted something that had the multimode similar to what my 3rd gen currently has (VF3AM).
Best I can tell, the 3rd gen 4Runner multimode t-case (VF3AM) will not bolt up to the 5th gen transmission, but the 4th gen multimode t-case (VF4AM) should bolt up. The 4th gen's VF4AM t-case would be able to offer 2wd, 4Hi (center diff unlocked, aka AWD mode), 4Hi center diff locked (true 4x4), and 4Lo with center diff locked or unlocked. Looks like the best candidate for this swap would be a 5th gen SR5 model that has the all electric 4wd selector, because the VF4AM is also all electric (no manual t-case shifters), and the SR5 already has an ADD front axle (Limited models with the VF4BM t-case do not have ADD because they are full-time 4wd). The stock 5th gen SR5 4wd ECU would need to remain in place, as it apparently talks on the CAN Bus network. The 4wd ECU that comes with the 4th gen 4Runners doesn't appear to connect to CAN Bus based on the wiring diagrams I've looked at. With some repinning of connectors at the t-case actuator, it appears that the 5th gen 4wd ECU in the SR5 controlling the VF2 t-case can control everything in the multimode VF4AM (ADD, Hi/Lo range selection) except for the center locking differential. It would appear that the center locking differential would have to be controlled outside of the 5th gen SR5 4wd ECU. This could potentially be accomplished the same way people use aftermarket wiring harnesses to control retrofitted factory rear elockers. When I retrofitted in my Toyota factory locking rear differential into my 3rd gen, I ordered an aftermarket wiring harness to control it. The harness is controlled by the push button RR Diff Lock on my dash, and uses the limit switches in the locking rear diff to know when to cut power to the electric motor. Such a harness could be easily modified to control the center locking differential in the t-case. Due to the longer length of the VF4AM multimode t-case, I believe one would need to source some 5th gen Limited front and rear driveshafts, since the Limited models came with the VF4BM (full time 4wd t-case).
All of this is theoretical based on the research I've done on the topic. I have no real world experience with this swap.