a) there's basically two versions of DVI, single- and dual-link. You need dual-link if you want to run insane resolutions
. Two outputs are normal for any recent graphics cards. Also, if you only have analog monitors (regular VGA/D-SUB), don't despair, cheap dvi->vga exist, and most cards today come with at least one.
b) hm, onboard graphics that comes with HDMI
? fancy. I have no experience with HDMI, so can't really comment on that... but as long as you can connect your monitor to it, you should be just fine
c) as long as you get the right type of harddrive (IDE vs. SATA), it's really a no-brainer... it's just about impossible to mount harddrives wrong. For IDE drives you'll have to worry about MASTER/SLAVE jumper setting, for SATA drives there's no such thing, making it even simpler.
Personally I'd go with an nvidia based card instead of ATi, I've had bad experience with ATi drivers... I'm currently running a passively cooled GF7600, and it works just fine.
Since you're getting a discrete graphics card, don't worry about onboard graphics for the motherboard... I'd go without, personally (although it could
come in handy if your graphics card blows up).
Any reason you're going for AMD64 instead of core2duo? price?
. Anyway, if you do go for AMD64, be sure to get a motherboard with socket AM2.