There's not much you can do to the 3.0 v6 to make it great. In stock form it lacks, and unfortunately even the common aftermarket parts don't do a whole lot to wake it up. You can attempt to turbocharge the motor, but be prepared to replace head gaskets regularly.
I'm not sure what gear ratio you have, but I recommend 4.88 gears for a 3.0L/5spd with 33" tires. The rolling resistance of a mud terrain, combined with the larger circumference and additional weight of the tire are just too much for the 3.0L to happily handle with stock gearing.
As for possible motor swaps, I would urge you to go big, or go home on such a thing. If you are prepared to undertake a motor conversion, why not convert to something newer and more powerful such as the DOHC 3.4L V6 from the Tacoma and Gen 3 4Runner. The wiring will be the hardest part, as the 3.4L runs OBDII (on board diagnostics 2nd generation), but it is still very do-able.
