The PC you and your friend is trying to build is rather expensive.
Motherboard: Great, but unnecessary if its expensive upper-end features aren't going to be used.
Graphics Card: Expensive. Minimal performance boost over the 8800GT, but costs way more.
Enermax: That's one expensive and powerful power supply, but you would be fine with something like the Cooler Master Real Power Pro 750w (if you don't mind that it's not modular, so lots of cluttering sleeved wires). CM RPP 750w isn't compatible with MSI motherboards though, but you should be fine with your listed motherboard.
CPU: No comment
Hard Drive (Raptor): Overrated, it helps with loading any software including the OS. If that justifies the price for you, then go for it. (Don't worry that it's only SATA I because hard drives overall don't read or write very fast at all even when spinning at 10,000RPM. The SATA I interface transfers at a max rate of 1.50 Gb/s, which is about 187.5 MB/s. That's a lot. When I try to read or write on my 7200RPM 320 GB seagate barracuda hard drive, it reads and writes at 60-70 MB/s max at the same time.You can try copying and pasting a large program file on your hard drive to see for yourself.)
Hard Drive (Caviar): No comment.
Monitor: No comment.
OS: No comment.
There are no difference in performance between 2x2GB rams and 4x1GB rams, so long that they are inserted in pairs for dual channel. DDR3 rams are overpriced and will yield no more than a 1% increase in overall system performance over the slowest DDR2 rams. Rams are so fast that it is even trivial to upgrade from DDR to DDR2 rams because rams are bottlenecked by the hard drives that stores all the information the rams need to retrieve from.
For your case and fan question, it depends on the size and speed the fans are spinning at. Also, mid size chassis is vague, some mid size chassis are huge, others are smaller. Giving the dimensions of the chassis would be more helpful.
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