Unfortunetly this is not your grandad's big block chevy. You can't open up the valve seats to fit newer/wider intakes on them like you could in the old days.
You can add a supercharger, get a stand alone computer unit to manage the fuel and so on. Upgrade the fuel pump & filter to match the new components; in my honest opinion you have no business putting a turbo or supercharger on an NA engine without rebuilding the bottom and top end to handle the boost and extra power you want. They stopped supporting the TRD Supercharger for the 4.7L (2UZ-FE) because the Tundras would blow motors at "stock" boost (granted they were American made engines vs. the Japanese built Land Cruiser & 4Runner units.)
The transmission can probably take something like 400ft.lbs. of torque before it starts getting strained (just a guess, not really backed by anything.) Transfer case should be okay, though if you're going for more power you're better off updating the transfer case to a beefier unit to handle the extra torque. Our rear axles I've heard aren't as robust as say a Ford 9", there are companies that make replacements that will handle the stress. Currie (SP?) makes some neat units for the FJ (120 Platform also, will fit fairly close.)
In the end if you're looking for more than the, lets say 5hp/3ft.lbs of power at the rear wheels (which is gonna be what your mods have really netted you if that, to be honest with you.) You need to spend serious money and thought into not only beefing up the engine output the rest of the vehicle to handle your goals.
I am not trying to turn you away, its just a lot of people like to "tune" their cars but end up having no idea what truely "tuning" or getting performance out of a vehicle really means. Its all a balancing act, there's a reason a Corvette ZR1 is built the way it is vs. some shmuck who tosses a supercharged LS3 into his Camaro.