An upgrade such as a larger throttle body is only going to improve performance if the existing throttle body is the main restriction in the intake system. If the intake manifold, intake tubing, or air filter assembly creates more of a restriction then there's nothing to be gained by a larger throttle body.

95 Montero SR
3.8 MIVEC, Advance headers, 2 1/2" exhaust, Magnaflow muffler, OME shocks & rear springs, 2" body lift, 3" tank lift, 4.90s, TRE front locker, factory rear locker, Roger Brown Rock Sliderz, 315/75r16 (35") tires, Sport big brakes