I think to get any sort of stock look to your car, you're going to need an in dash CDP. I would opt for one of the less flashier ones, possibly with a digital out if you can find one.
After the CDP, you can run it into your own preamp of sorts, just set the CDP to it's highest unclipped output, and put a pot inline with the preouts, mount the pot in the dash, and add your favorite stainless knob and faceplate. This can go to a DAC if you wanted, yes, there are a few out there for car audio, or mod your own if you so desire... shouldn't be that difficult.
Then you can go to your favorite high quality amplifier, and do what you want with the speakers. I favour kick panels a considerable amount, although the extra work and time spent on them, and the room they require, is usually less than ideal for the average daily driver.
This is just my opinion of what I would do... heck this IS what I do, and I think it sounds fairly nice.