All my speakers essentially went out about a year ago. I found a couple of websites that you may find helpful. The first is technicalhelp4u.com which provides wiring diagrams for both the Pioneer and Nakamichi systems.
Another website, carstereohelp.com, states that a mute wire (which can be seen on the wiring diagrams referenced above) sometimes becomes grounded causing the speaker cutout you're referring to. It gives directions for checking a couple of connectors under the rear seat.
If that's not it, the problem is probably a failed amplifier. The carstereohelp website provides directions for pulling out the amplifier which is located under the CD changer in the trunk. I called my local Lexus dealership, Lexus of Annapolis, who said they could replace the amp without a rebuilt amp for $700 with a turn-in of the old amp. Seemed a little high to me. Carstereohelp offers to rebuild your amp for $350 if you send it to them. I'm trying to find out if I can put in any replacement amp.
Any ideas?