Your questions are answered elsewhere in the forums; a quick search will get you more information than I'll be providing.

I would start by getting a more modern motherboard. Old hardware is near the end of it's life, most likely. But what you've got meets the nminimum specs with plenty of headroom, so you should be fine for now.
WHS will see your disks during installation if they are either configured in the BIOS in what's usually called "Legacy IDE" mode, or if you supply appropriate drivers. So if you don't supply the drivers for your PCI SATA card, then WHS won't see them at installation. That's not a problem; you can add the drivers later and WHS will see the drives then.
If the system disk dies, you replace it and do a "server reinstallation". Assuming your WHS wasn't so full that the server was storing the only copy of unduplicated files on the system disk, you will not lose any data.