Starterwiz

I'd agree that the stock unit's integration into a system would be a good thing on many fronts. Cosmetically well designed, less chance of attemted theft, and potentially saving a buck to spend elsewhere.
However, while the preamp components of most head units are decent, the output stages are usuallylimited in their bandwidth, as they are designed to be used by the avereage "ignorant" consumer, on speakers with poor to no low bass response. If those outputs had the ability to play full power down below 20hz, there would be a lot of warrant work at the dealer level replacing tweeters and speakers from the people that play their systems full blast.
Taking a signal from those outputs is not likely to yield as clean or flat a signal as a pure preamp output that has not been through two or more extra stages of processing.
That being said, I've not had a chance to play with a Clean Sweep yet, so I may change my tune, but my experience to date with high level type inputs has been less than satisfying.

Any system is only as good as the weakest link.
The design and installation are the most critical, and deserve the utmost care and attention.
Finding a good, honest installer is not an easy task, but we are out there. Someone that will take the time to skin a door panel for you, and see what speakers can be made to sound good in the available space, rather than have a salesman stand at a board, pitching the benefits of a particular speaker without ever having even looked at your car, would be a first clue. I never recommend a high end speaker without first seeing what kind of install is required (spacer rings, speaker to door panel sealing, improving the baffle, etc.) It has to be part of the overall budget.
Then I will always recommend the best sounding speaker I have available for the budget available. That may not be the best one on the market, but the best I have. No shop can carry every brand, but if you reward your installer, by buying all your stuff from him, he will likely be more apt to care that "his" stuff ends up sounding better than his competitors....win, win.

Shop around, hang out a bit, see some jobs in progress, some completed jobs, and you'll soon know who's got the right stuff.... and when you find a good one, the word...

S.F.W.

Thanks for the advice. I will start looking ofr my installer, then plan the car with their assitance.
My main goals are clarity, not so much volume.
I'll keep everyone posted on how I progress.