Most of the V6 5-speeds I have seen have the 4.10 ratio. It meant choosing Extra Value Package 4 (called the Sport package in later years), and many were equipped this way. The ones that don't have it generally have 15" split spoke wheels on the tiny street tires and no fender flares at all (no chrome strips, no black flares, no body colored Limited-style flares). See pic below.
Here are the production numbers for the manual transmission 3rd gens, in percent of sales
1997 Toyota 4Runner - 5 Speed Manual 11.4%
1998 Toyota 4Runner - 5 Speed Manual 8.0%
1999 Toyota 4Runner - 5 Speed Manual 4.5%
2000 Toyota 4Runner - 5 Speed Manual 2.9% (last year offered)
So not only are you trying to find a needle in the haystack with the 5-speed, finding one with a locker on top of that is even harder.
To get the locker you had to order an SR5 4WD with Extra Value Packages 4 and 5. Package 5 was the stand-alone locker option for the 4Runner. This is taken from the 2000 order sheet.