Your project will take some research. Bear in mind that computer technology doubles every 18 months, so trying to keep up is like "spooning against the tide".
Decide how much money you want to spend, then break it down into catagories
I would say start from scratch as you will have more flexability when it comes to upgrades. Just make sure that all your components are compatible. If you are uncertain, simply post them on this site requesting feeback and you will get it.
Consider thermal management. The Case is important for good airflow. Make sure that there is an intake in the front and one in the back, 120mm is cooler, but louder. If you can get a Case that has a blowhole.
Start compiling a list and the toss it our way if you need feedback.
[SIZE=\"1\"]E6400 @ 3.4 , Noctua 120
7900GT @ 670/1680 , VF900
2 x 1GB Patriot 6400 @ 425
WD SATA 250GB
Neo HE 550
P180 / G15 / MX1000[/SIZE]