If the rig came stock w/31's it would have 4.87 gears, and the door code would be G14, and the 4.56 gears would be G25, or possiblyG28 for 4.30 gears depending on the truck or 4-Runner. My 5sp 3.0 X-cab was never that slow compared to my 2wd 22r, and from what I remember wasn't as slow as my sisters '95 auto Runner.

If you don't have factory 4.87 gears for the 31's intalling them will bring the truck back to factory tire to gear ratio, however I would recommend installing the the 5.29 gear set. The 5.29's gears should work better for the 4-spd tranny, if it is geared a little to high you could install a set of 32" tires.

When the 3.0 engine was introduced it wasn't slow at all compared to its domestic counterparts that gad a v-6 engine, and was likely de-tuned for the truck since the camry engine from the same era had a much higher hp output. Also when the engine was introduced in '88-89, consumers weren't after fast trucks, not even full sized v-8 rigs were being sold as performance vehicles.

There are mods you can do to helpo it perform better, but they are not cheap. I would open up intake, and rework the exhaust(under $500) Other upgrades include the ignition and geaders(looking at about $1500), though regearing would be your best bang for the buck.