My previous truck was also a '99 Limited, but I didn't have the locking rear differential on mine. With that being said, the thing felt like a tank when it was in 4WD. Unfortunately, my old truck met an untimely demise when I got broadsided by someone running a red light in Boston, hence the move to a 4th generation.
RIP
About 18 months ago I picked up a 2006 Limited with the V6 and I'm still completely in love with it. It starts easily, idles smoothly, shifts well, gets so-so gas mileage (19-21.5 average), has no squeaks or rattles, looks great, and has all the creature comforts I could ask for, i.e. heated seats, power everything, leather, sun/moonroof. I installed an aftermarket head unit so I have Sirius/XM and full Bluetooth connectivity for both phone and music streaming.
I bought it with 73,000 miles on the odometer even though the CarFax showed an accident in its history. I randomly selected a Toyota dealership near where it was for sale and had them do a full-blown inspection and they told me I had nothing to worry about regarding the accident, that it was fixed properly. I've now got 103,000 and it's running like a top.
I'm partial to the '06-'09 model years because that's what I've got, but I do like the projector headlights, the LED taillights, and the general aesthetic of those years. That said, I don't think you can go wrong with the 4th generation.
In addition to the issues listed above regarding seized calipers, transfer case actuators, etc, with the V6 I'd have them pull the #6 spark plug out for you so you can inspect the threads and see if there's any evidence of oil contamination before you purchase one. There's strong evidence at this point that the 1GR-FE engine has a problem with the head warping if it overheats, and possibly even when it doesn't, so make sure everything's ship shape in advance. Otherwise, it's an awesome rig.
As far as maintenance goes I've replaced the spark plugs, just replaced the rotors and pads up front last week (no seized calipers here), keep Mobil 1 in the crankcase, differentials, and transfer case, and flushed and changed my coolant last summer. Next on my list is change my brake fluid and throw a new serpentine belt on it, but otherwise everything seems to be good on it. I've had two check engine lights since I got it, but both times it was caused by my failure to fully tighten the gas cap which resulted in evap codes being thrown. Fixed itself both times once the cap was tightened.
I know this is TL;DR, but it's a great truck and I endorse it fully. Plus, this forum probably has a DIY write-up for anything you'd ever want to do mechanically or mod-wise, so your'e in good hands here. Good luck, go 4Runner.
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