I also had a 95 4runner with 3.0.  I put a 2" body lift with 33" tires, i had the stock 4:88.  Power wise there was a noticeable difference, however it wasn't a complete night & day.  It was a little difficult getting pn the freeway if the on ramp was up hill but on flat land i didn't have a problem.  But there was a difference from the 31".  Mine was a 5 speed and not the automatic, but had a buddy that put a 4" ProComp lift with 33" on his with an auto and he had some power differences but i was happy with my body lift, on the trails it kept me lower to the ground and my center of gravity lower especially with the IFS.