When I bought my 96 - 4 Runner way back then, that was the first thing I did. I gutted that so-called sound system. Ripped out everything, head unit and speakers. I replaced the head unit, with a dual DIN unit. I replaced all 4 speakers. I also added a SUB and two amps. I placed the 2 - amps under the front drivers seat. One for the speakers and one for the sub. Placed a 12 pak CD changer under the front passenger seat. Replaced ALL wiring, speakers, power, everything but the antenna wiring.
Love it and haven't had one problem with any of them toys.