Just for fun, I threw together some stuff on Sonicelectronics.com. They have good deals sometimes. I am sure you can find better ones.
This would be a major upgrade over the factory system, you could always spend more, you can probably spend less. Its not top of the line, but everything is an improvement over stock.
Here is an example of what you need to buy:
5.25 component speakers $149
6.5 inch sub $79
JL 360w 4 channel amplifier. $239
You will also need a trim ring for the sub: $12
Amp installation kit: $18
You will also need some RCA jacks: $3
Spade connectors: $3
You should also go to home depot and pick up some silicone...
GE Silicone 2.8 oz
You can freak out and spend alot more, or you can waste a **** ton of money and pay someone to do it, but for around $500 you can replace everything with good quality, BRAND NEW stuff.
Its not hard. Just dive in.
THIS IS ALL YOU NEED!