Whats the 4 banger the 90-05 has?
The 79 to 87 trucks had the 22R, a 2.4L carb'd 4 cylinder. Some 85 to 87 had an early 22R-E, fuel injected version of the engine. A very few of them had a 22R-ET, turbo charged version of the EFI engine. This is a very rare one.
By 1988 the trucks all (well 4WD anyway) had 22R-E or the 3VZ-FE, 3.0l V6.
BTW, the first generation 4WD is 1979 to 1983. The 2nd generation is 1984 to 1988.
The 3rd generation 4WD trucks are 1989 to 1995. These all had either the 22R-E or 3VZ-FE.
In 1995 the Hilux truck was replaced by the Tacoma in North America. The 1995 to 2004 represents the 1st generation of Tacoma. They had the 3RZ-FE 2.7L 4 cylinder or 5VZ-FE 3.4L V6. Some 2WD trucks may have had the 2RZ-FE 2.4L 4 cylinder. All of these have a power bump compared to their previous engines.
What is different here is the drivetrains. The 22R-E and 3RZ got a G-series or W-series transmission and RF1A transfer case (in the 95 and older). The V6 engines (and the turbo 4 cylinder) got an R-series transmission behind it and a VF1A t-case (the Tacoma also got a chain t-case on both engines). The difference is the RF1A is a totally gear driven transfer and the VF1A is a chain driven case. The tranny bell housings and the tailshafts don't mix, either.
Point here is swapping a 4 cylinder for a V6 requires a lot of work, moving motor mounts, moving the cross member under the t-case, moving the holes in the floor for the shifters, etc. It's quite a bit easier to swap a newer 4 cylinder for an older one. If that's not of interest and you're dead set on ditching the 4 cylinder altogether it makes just as much sense to think beyond Toyota, a 4.3L Vortec V6 from a GM, a 2.8L Cummins, a small block Chevy.
FWIW, I agree with Clutch, if you want a 3.4L V6 get a nice 1st gen Tacoma and do other mods (such as beef up the frame) rather than ******** with trying to get the right combination of drivetrain parts and troubleshoot the wiring harness you had to hack out of a wrecked 4Runner to get the 3.4L. If you already had a decent 79-95 it would be a different story.