And for the other post about sound fading out then not playing, that sounds EXACTLY like a burnt amp!
When speaker coils are fried, they will pop and crackle as the cone floats in the magnet. If it has a break in the coil's wire, it will hit a spot where it just stops working completely, until you either overcome it with current (turn the volume up higher) or you physically move the diaphragm.
When it starts off softly, then fades out to nothing, that says blown amp. Turn key off, wait a minute or two, then turn on again, see if it does it again. If it does exactly the same thing, that's definitely a blown amp.
You can further check this if you have enough knowledge of car audio, and you're comfortable with wiring. Reading your comments, I would suggest you not do this yourself, as this would require intercepting the output from the head unit by pulling pins on the rear output connector and wiring up a speaker to the output to double-check for sound directly from the deck. While you could do this at a door or the hatch, this will not determine if there's still a short somewhere else. Wiring directly to the deck will immediately tell you whether the amp is good and its a wiring or speaker issue, of if the amp is bad and you need to repair or replace it.
Furthermore, if it is the amp, the next question would be why it blew! These systems are made to take abuse, otherwise you'd hear about tons of 4 runner head units being repaired at dealerships all the time! So, slapping in another head unit (they're cheap online, 150 ~ 250 for replacements) is not wise to do. Find the problem and fix that first.
I'm gonna go out on a limb here and guess that you like to play your music really loud, probably with the hatch open and blaring loud at a park or beach, right? Aside from blown speakers or a shorted wire somewhere in the vehicle, playing the stereo loud for hours at a time in an enclosed dash will eventually fry the amp, literally! There's no place for the heat to go in an enclosed dash, even if you have the windows opened. Sooner or later, it will burn the power transistors out, and it makes perfect sense that it would be the rear channel, as it has more load on the system (4 full range speakers for the 2 channel rear amp, vs. two speakers in the front doors and that capped tweeter-like speakers in the dash).
