Don't replace the factory sub, just add 12s later.
I'm making this list based on the assumption that you're running an aftermarket head unit with a built in (very small) amp. For $1150 I built a system sans head unit and install gear.
Amp, 100W RMS @ 4Ω bridged on, $150
http://www.sonicelectronix.com/item_21951_Kicker-ZX650.4-10ZX650.4.html
Front Comps, $190, bridge amp for these, they're only rated to 85W RMS, but they'll take 100W no problem
http://www.sonicelectronix.com/item_19750_Boston-Acoustics-SR60.html
Rear Coaxs, $65, run off of head unit power so about 15-20W RMS, rear speaker are just for fill, don't spend a bunch of money on rears
http://www.sonicelectronix.com/item_5022_Boston-Acoustics-S65.html
Sub Amp, $350, 1000W RMS @ 2Ω
http://www.sonicelectronix.com/item_21957_Kicker-ZX1000.1-10ZX1000.1.html
Sub, $400, IDMAXs will get loud but are extremely clean sounding
http://www.sonicelectronix.com/item_20482_Image-Dynamics-IDMAX12-V.3-D4.html
That leaves you at $1150. I built this with SQL in mind, loud but still clean, it will get plenty loud but sound clean while doing it. Build a 2.5 ft^3 box ported at 30Hz for the sub, and then spend some money and do a Big 3 upgrade, and use the rest of the budget on wiring. You should come out somewhere around $1300 for all of that if you do the install and box build yourself. I only put ONE twelve in the build, 1000W on a good 12 (like the IDMAX I suggested) will be superior to two cheap 12s on 500W a piece. To increase your SPL 3db, you must double your wattage, or double your cone area. So mathematically, 1 12" on 1000W will be nearly as loud as 2 12", and sound much better while doing it.
I wouldn't recommend Infinity speakers if somebody recommends them, the titanium tweets are harsh. Focals are nice but you have to hear them before you buy them, they have bright sounding tweeters that many people don't like.