All right, you also mentioned comments about building from scratch, so thinking about the CAD you'll be doing...
AMD Athlon 64 X2 6000+ Windsor 3.0GHz
Newegg.com - AMD Athlon 64 X2 6000+ Windsor 3.0GHz 2 x 1MB L2 Cache Socket AM2 125W Dual-Core Processor - CPUs / Processors
$153.00
GIGABYTE GA-M57SLI-S4 AM2 NVIDIA nForce 570
Newegg.com - GIGABYTE GA-M57SLI-S4 AM2 NVIDIA nForce 570 SLI MCP ATX AMD Motherboard - AMD Motherboards
$84.99
G.SKILL 2GB 240-Pin DDR2 SDRAM DDR2 800
Newegg.com - G.SKILL 2GB 240-Pin DDR2 SDRAM DDR2 800 (PC2 6400) Desktop Memory - Desktop Memory
$85.98 (for w)
Antec Nine Hundred Black Steel
Newegg.com - Antec Nine Hundred Black Steel ATX Mid Tower Computer Case - Computer Cases
$119.99
Western Digital Caviar SE WD3200AAJS 320GB 7200 RPM 8MB
Newegg.com - Western Digital Caviar SE WD3200AAJS 320GB 7200 RPM 8MB Cache SATA 3.0Gb/s Hard Drive - Internal Hard Drives
$139.98 (for two)
SAMSUNG Black 20X DVD
Newegg.com - SAMSUNG Black 20X DVD+R 8X DVD+RW 12X DVD+R DL 20X DVD-R 6X DVD-RW 12X DVD-RAM 16X DVD-ROM 48X CD-R 32X CD-RW 48X CD-ROM 2MB Cache IDE 20X DVD±R DVD Burner - CD / DVD Burners
$22.99
PC Power & Cooling S75QB 750W
Newegg.com - PC Power & Cooling S75QB 750W ATX12V / EPS12V Power Supply 100 - 240 V UL, ULC, CE, CB, RoHS - Power Supplies
$149.99 ($30 mail rebate not included)
EVGA 512-P3-N871-AR GeForce 9800 GTX(G92) 512MB
Newegg.com - EVGA 512-P3-N871-AR GeForce 9800 GTX(G92) 512MB 256-bit GDDR3 PCI Express 2.0 x16 HDCP Ready SLI Supported Video Card - Desktop Graphics / Video Cards
$299.99
Microsoft Windows Vista Home Premium SP1 64-bit
Newegg.com - Microsoft Windows Vista Home Premium SP1 64-bit English 1pk DSP OEI DVD - Operating Systems
$99.99
ASUS Arctic Square 92mm
Newegg.com - ASUS Arctic Square 92mm Vapo Bearing CPU Cooler - CPU Fans & Heatsinks
$44.99
Arctic Silver 5 Thermal Compound
Newegg.com - Arctic Silver 5 Thermal Compound - Thermal Compound / Grease
$5.99
SAMSUNG Black 1.44MB
Newegg.com - SAMSUNG Black 1.44MB 3.5" Internal Floppy Drive Model SFD321B/LBL1 - Floppy Drives
$6.99
For a system with technically the same stats as the one you mentioned for a total of
$1214.87 without S&H and Tax depending if you live in a Newegg hub state.
That's almost half than the one you were looking, so if you know how to build and troubleshoot (in case parts arrive DOA or malfunctioning) then you can do it yourself and save almost a grand. Of course we're here to help with troubleshoot (look at some of the threads, Pwn and Fluffy doing a great job at it) if you ever need it.
Now, why I picked what I did:
1.- CPU: Always loved AMD (I'm so bias), they are not as fast as Intel but pretty close for a lot less.
2.- Mobo: Same, Gigabyte has never let me down (while ASUS burned 3 different cards) and considering that you wanted 2 16x I had to go with Dual core chipset, I wanted to give ya Tri or Quad core CPU but atm the mobo for those are a shot in the dark and the only ones with 2 PCI-E x16 were getting horrible reviews.
3.- Case: Best case there is for air movement, no question about it, think half if not more of the PC builders in these forums use this case.
4.- RAM: Best bang for the buck, not to mention that 2 of these means you can get two more later on because you're not sticking 4 1gig sticks.
Everything else is just good quality parts. Now many people ask me why a floppy drive? that's obsolete, well it's still the most reliable and widely used (no matter the ae of the PC) backup device, not to metion you taking CAD means yer in school, and I know CAD files won't fit in there but probably other school projects will.
Now the cooling, usually with this case you don't need an aftermarket CPU heatsink, but you will be using CAD thats a lot of processing power which generates extra heat, so this should help
Oh and you mentioned liking to record your guitar on the PC, well the mobo has a 7.1 integrated sound card
Another thing we don't put in PC templates is keyboard/mouse/monitor unless requested.
All right, I'm hoping some of the other guys drop in and trow other templates (usually better than mine) and hopefully help you further.
*leaves the floor*