Head Unit: Pioneer Premiere 940MP -www.thezeb.com - $550
Components: CDT Eurosport ES-620 - $540 ( These are just a suggestion, you could look into a thousand speakers with that much money, search teh board for Focal, CDT, Rainbow. )
Subs- Stereo Integrity Magnum d2 ($300 x 2= $600)
Build a box for them, i think sealed for your purposes.
Box Cost ~= 60 Bucks after carpeting (Or Have Donn Make one for you)
Component Amp: Hifonics Zeus ZX6000- $440
Sub Amp: Hifonics Brutus BX1500D- $580
Wiring:
http://www.knukonceptz.com
1 Guage Power Wire (2 Would be fine probably)
2 Sets of RCA Cables
Decent amount of Speaker wire
Remote Cable
Just install yourself, it really isn't very hard. If you really don't want to do it you could get a shop to do it, but they are going to bend you over on install fee's when you don't buy stuff from them. Maybe have them install components for you if you have them do anythign because that will be by far the hardest part. Also what kind of car do you have?
Total=$2850 So a grand or so under your budget, with that thousand dollars you could probably have a shop install it for you, but it really isn't worth it. Your system will sound very good, and those subs will pound and sound very good in the process. Good Luck
-Jason