[thstone]

My first thought is to further investigate the aftermarket stereo. I would track down/trace the power wires for every component in the stereo system.

The installer may have connected the stereo (I use this word generically to mean any or all of the actual components) direct to the battery or to a wire that connects direct to battery power without going through the stock fuse panel in the driver footwell. If this is the case (and the installer knew what he was doing), then there is likely another fuse block or inline fuse for the stereo power that is in parallel with the stock fuse panel.