Leave the stock radio alone.

Add an amplifier to drive the 6x9s and possible other speakers up front (kick panels) or possibly component speakers hidden somewhere.

The input to the amp could either be a bluetooth adapter that would allow you to stream wirelessly from a device or a hard line connection, something like a cable run from the input side of the amp up front, RCA to mini plug stereo adapter or similar. There are likely iPod specific adapters out there as well, if he is a true apple fanboy.

The bluetooth or mini jack option allows you to use many devices, could stream pandora from cell phone, etc.