How hard would it be to swap a Auto trany with a manual tranny in a 94 v6 4-runner? Would it be worth the work?

 

I would suspect that it may be cheaper and more efficient to just buy trade auto for manual...

 

you'll need:

5 speed tranny and transfer case(duh)
clutch gear(clutch set, hub, clips, fork, line, master/slave etc)
pedal assembly from a m/t vehicle of the same generation(i suspect that an '89-95 truck would be a donor)

it's a bolt-in swap, except for possibly cutting new holes in the floor for shifters. you'll also have to bridge the wires on the neutral safety switch so the ECU won't think you're in park and not let you start the engine

 

you'll need a flywheel and I'm pretty sure the manuals and autos had different ecus

 

in addition to the other stuff already mentioned, of course