Cannot Boot Windows

I consider myself an experienced system builder, as I'm a computer science major, I built my own system, and I built my brother's system from hand-me-down parts from my system. Until recently my brother had been using a system I built for him housed in an old HP case which was fine, but not great. So I got him an Antec Nine Hundred for Christmas and we moved everything over, and the only thing that changed was the number of fans...but now I can't get Windows to boot. When we first tried booting up from the main hard drive, the following was displayed after POST:

boot0: MBR
boot0: done
BOOTMGR is missing
Press Ctrl+Alt+Del to restart

First I tried using the Windows 7 Installation disc to repair, and was a bit annoyed when it took 2-3 minutes to load up, and then sat on that blueish background for another 10-15 minutes before the first prompt appeared (it has since ALWAYS taken this long each time I've booted from that disc). I tried "bootrec /fixboot" but it didn't change anything. Tried changing the main HDD to a different SATA port but that didn't help either. Then I tried to reinstall Windows and it seemed to fly right through the first step..."preparing files" or something...before reaching the second step and telling me that it couldn't find all the files and that I had the wrong DVD...which I don't... Anyways, I appear to be stumped and would appreciate any help. Here are my brother's specs:

Antec 900 Case
Asus M2A-VM mobo
AMD Athlon 64 X2 3800+
4GB DDR2-800
GeForce GTS 250
1x 250GB SATA HDD (boot)
1x 60GB IDE HDD
1x IDE DVD-RW drive