Just an update concerning this.
The machine annoyingly, does not recognize the new HDD (500GB), so I thought I'd swap the 500 for the drive in the network's backup machine and annoyingly, it doesn't recognize that either. It would appear, given it's recognizing the 40GB out of the test machine, that it only likes drives up to 80GB, which is a major annoyance. I was going to look for a BIOS update (board is an Asus A7A266-E), but the Asus support/download site is down (server too busy error).
I've got the OS installed, and am now installing all of the updates. Once that's done, it will be configured and have PHP etc installed, along with the usual security/monitoring stuffage, then have the hpHosts files put on (hpHosts files are actually on an old 10GB drive, but it turns out that's got bad sectors too - wonderful!).
I'm hoping to have the setup/configuration and imaging (will be done after updates/config etc) done by this afternoon, and the testing done by this evening. So all in all, if all goes well, the server should be back online by later this evening.