Just some points to consider before supercharging your engine:
1. Premium gas is required. It is a must! MPG varies with use. MPG drops like a rock when you do use it!
2. Automatic tranny fluid should be changed TWICE as regularly. In addition, a tranny cooler is highly recommended.
3. Many people would recommend switching to SYNTHETIC engine oil when supercharging.
4. More noise! Whinning and whirring.
5. You may lose LOW RPM power (below 2000 RPM)...SC's are best at boosting MIDrange power...they are not good at the extreme ends (high and low). Remember, SC's is powered BY the engine...therefore, it is always PARASITIC to your engine's power, which you will notice most at very low RPMs and high RPMs. (On the other hand, turbochargers [powered by exhaust] are very efficient and good for high-end RPM power BUT do suffer from some degree of turbo lag.)
6. Remember that SC will likely not be very helpful in off-roading because you need to press 3/4th of the accelerator to turn the SC on (according to JacksonRacing Eaton-Root SCs; not sure about TRD chargers)...in off-roading, if you do that, you will spin the wheels and lose traction! Power is not linear in that circumstance (because most of the time, you are not flooring the gas pedal).
7. Although argued by JacksonRacing & TRD, all force-induction system (turbos and SC's) will cause more wear-and-tear on your drivetrain. That is a given.
8. Of course, there can be many problems after installing the SCs...just read
http://www.gadgetonline.com/4Run.htm
In general, i am not a big fan of superchargers. I prefer displacement, especially in an SUV/truck. Since the '03 4runners already have powerful engines, i don't see SCs as a needed thing. There is no way the 4Runner will keep up with an BMW X5, even if it can accelerate the same. 4Runners are made for all-terrain adventure.
Just my opinion.