And my answer is.....
I'd get a different vehicle.


I know, I know. 3rd gen 4runners are awesome, I agree. Problem with the 3rd gens are:
1. The newest ones are now 9 years old and it's only going to get harder to find low-mileage examples.
2. Poor MPG+ less than stellar power + small gas tank = not a fun road trip vehicle.
3. Auto tranny is a known weak point especially on higher-mileage models.
(#1 is especially true of the hard-to-find manual tranny models since they were only 96-2000.)
I also think Toyotas are "overvalued" on the used car market. Compare prices between an Xterra and a 4runner and you can see that. Even if you think the 4runner is a superior vehicle, the price differences are dramatic. 3rd gen 4runners have a strong "cult following" which is good if you own one, but not so good if you're looking to buy one.
The newer gen 4runners don't appeal to me, they are too "car-like." I can't abide by getting a vehicle that I'd have to throw $1000 of suspension mods just to get it to perform the same way as my 3rd gen did out of the box.
Depending on my budget I would most likely end up with a 2nd gen (2005+) Xterra with a manual (6 speed) tranny. I would certainly miss things like the roll-down rear window, but off-road capability would be about the same and if I could find an "off road" model I'd even get an E-locker!
I think Nissan was smart to keep offering a manual tranny in the Xterra. Sure, you can get a manual in the FJ Cruiser but you also get full time 4wd, which I absolutely
don't want. Besides which, FJC's have their own "issues" (visibility, cargo access, etc.)