Well, you can make a custom baffle for 6.5" components. 6.5" inch are the most popular sized mid-range.
Do you want to do a 2-way front stage or a 3-way front stage?
(the difference is: 2-way has tweeter and mid-range woofer. 3-way has tweeter, mid-high and mid-low range woofer.) If you don't want to cut into your car (I don't blame you), throw up a price on what you want for speakers and I'm sure one of us can recommend something. Personally, I'm a fanboi of Hertz Audio. But everyone has their own opinions.
As for integration for your stock head unit. Pioneer makes an integration processor (you re-route the speaker wires to hook up to it, and it acts as an EQ (so you can go active, if you want) and has RCA-outs. This is a bit costly at $80 dollars. A cheaper alternative is something called a 'Hi-Low Converter'. You can pick them up at nearly any local audio shop. This does the same thing, except is lower-grade. You need one per pair of speaker channels, and it turns into one pair of RCA out. They'll cost around $20 bucks. As for the quality of either, I'm not sure. I've only used them on my brother's truck, and he didn't spend much on the system, so I'm not too sure on the quality.