When I started looking for a 4Runner in 2000, there were no stick shifts on the lot. I talked to the dealer. They just don't order stick shifts because of the demand. They also don't order 4Runners with non-powered windows. No demand for them. Also, it is very hard to special order a Toyota. I have not seen a stick shift, so they are out there, but "rare" is the key word.
I really like the second generation 4Runner, but I think the 3.0 V6 is the weak link to the design. They tend to be thirsty. Blown Head gaskets still happen.
http://atlanta.craigslist.org/car/589153858.html
The 3.4 is a sweet engine. Good power, runs smoothly and gets decent mileage. And I have seen some with high mileage, i.e. over 300,000 miles.
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2001 & 2004 Toyota 4Runner SR5 4X2
Both V6 and both Natural White
"Yeah, I like white and I like 4Runners"