OK ... Let's try to untangle this ...
The 1999 4X4 XtraCab was available in both 4-cylinder and 6-cylinder versions.
The 4-cylinder would have had the 2.7L 3RZ I-4 engine. The 6-cylinder would have had the 3.4L 5VZ V6.
Check the 5th character in the VIN. To the best of my knowledge it should be an 'M' if it's the 3RZ 4-cylinder and 'N' if it's the 5VZ 6-cylinder.
As of 1999, 'SR5' denoted an optional trim / accessory package, not a model. This package included SR5-specific external badges: 'SR5' for the 4-cylinder; 'SR5 V6' for the 6-cylinder.
There were two SR5 option packages for 1999 4WD Tacomas:
SR5 Package #1 - 4WD
Includes chrome plated package and rear bumper, Deluxe ETR/Cassette with four speakers, sliding rear window with gray privacy glass, CFC-free air conditioning, passenger sunvisor w/mirror
SR5 Package #2 - 4WD
Includes SR5 Package #1 with the chrome package replaced with color-keyed front bumper, valance and grille
In other words - the only difference in the two 4WD SR5 packages was whether the optional exterior trim parts were 'chrome' or 'color-keyed' (color-matched to the body color).
So ... (Assuming I'm interpreting your post correctly ...) either:
(a) Someone's swapped the tailgate badge from 'SR5' to 'SR5 V6' OR ...
(b) The wrong badges (and under-hood sticker(s)) were installed at the factory OR ...
(c) This truck has had a motor swap