Rear Disks Caution!
I just did this swap and wanted to throw in a word of caution regarding the rear disks. For the record, my 4Runner is a 2006 Limited that had the upgraded 'Sport Brakes'. I used 5th gen (2010) TRD pads along with Napa remanufactured calipers and ultra premium coated...
It sounds to me like you're pushing the amplifier into clipping and its still not enough power to properly drive the aftermarket speakers. Clipping occurs when an amplifier is pushed to its limits, so the signal gets 'truncated'. Think of audio as a sine wave, and now imagine that you remove...