It sounds like you are looking to get good audio quality being able to use your factory stereo?
Out of curiosity, does that stereo offer the ability to use a CD Changer? Most do, some people don't realize.
I have a 2006 Honda Civic. I wanted both Sirius Radio and at the time, my iPod to be able to play on my stereo without an FM transmitter. I had a jack, the installer turned it into a toggle switch. He split off the CD Changer Aux in to 2 devices, and the toggle switched between the 2.
After a while the cable created a horrible sound quality, so last week I got a great setup that seems very universal, and I never had to switch to an aftermarket stereo.
Either way, go to bestbuy.com and navigate to their iPod and MP3 Player car connections section and you will see a number of solutions. Crutchfield is not bad either.
Good luck.