Hey M45ATL - I am sort of a self proclaimed expert on the 2003 M's.. I have done extensive work on the audio system, and can pretty much answer any questions out there. For more detail, check out my webpage on my installs and this may give you a good idea of what is involved with doing a system in the M. It's rather long, but should help.
http://thegreenm45.itgo.com/Audio.htm ( sorry about the pop-up adds... have moved it from my personal webpage to a dedicated site for the M, which I am not paying for, thus the ads.)
Long story short.... In order to replace the factory speakers, you need an aftermarket amp, you can simply patch into the signal that is being outputed from the stock Bose unit, however you will have what I call frequency attenuation at certain volumes. The louder the system goes, the less bass and the less high frequency inforation will get to the speakers. Bose has done this to protect their cheap speakers, but if you can live with that. An install shouldn't cost anywhere near the price you are being qouted. I am in the moddle of revision 3.0 on my system (which doesn't appear on the website yet), and after it's all said and done if I was paying retail, it would be a nearly $15000 system, the biggest part of that is about 40 hours of labor creating, sanding and finishing the two sub enclosures on either side of the trunk. At $9000 for a "basic" install, those amps better be gold plated? Whats this shops hourly rate? I am basing my system cost estimates at $70/ hour...... A simple install of front and rear doors, dash tweeters, a sub and amplifiers , with some sort of LOC to connect them to the Bose amp, shouldn't be more the $1500, plus the cost of equipment. Even that ($1500) for a basic install is high.
If you have any questions feel free to contact me.