Me and my friend was trying to install a radio in his 00 4runner, and i was wondering if it had a factory amp also, he has the 6 speaker sound system and the cd player doesnt work. We got a wiring harness and it wont plug up to the factory wires. I thought it might be like our cars.

you will need the appropriate amplifier integration harness in order to use an aftermarket stereo in conjunction with the stock amplifier and speaker system.. i had to use one for mine.

i bought mine from here and it came really fast.. this 'could' be the one you need.
http://www.audiooutfitter.com/70-8113/metra/p733474.html