Ya definitely use a brand new drive for your main, dont frankenstein your old one as your primary. Also I would probably add that you get a third drive since the two you got are huge, thats allot of wasted space for a primary drive. If you store lots of files or render to disk, you should be storing and rendering to seperate drive anyways. I'd use those two 1tb drive as storage and get a 550 or 750 gig for the primary. 

But, wow, they saw you coming.

Mobo, $250
QX6850 - $1030.
OCZ ram $185.
GPU $720
xp pro 64 $140
X-fi $70
dvd/cd $50
PSU $220
WD $300 x2
case $150

total $3415

And that's newegg as of tonight and prices rounded up. You could have ordered it, had it shipped in three days and paid the neighborhood kid $100 to put it together.

But still. Good rig. I built one around the same Kentsfield cpu and added a core 2 duo 2.16ghz laptop and I only paid $3800 total.

It does pay to shop around.