With RAID 1, you should be able to boot from either one of the hard drives. Degraded RAID 1 won't cause OS boot failure. However, in you case seems you have corruption in file system.
I suggest you connect the two drives one at a time and see if one of them can boot successfully. If yes you can add a new drive and rebuild the RAID. If you you'll need to fix your filesystem first by booting to OS CD and load F6 driver.
Thanks for your help on this. We put the secondary HDD into the primary slot and rebooted. The OS came back up, but with a couple of TCP errors - DHCP, IIS, WINS services (even though we aren't using it) etc were all failing, but we have resotred the IIS Metabase, and reconfigured DHCP, so it looks like we're back on track. Hopefully we're at the end of our troubles here - bullet dogged, but would have preferred it everything worked first time.
Thanks for the advise as well, we will keep these in mind going forward and use your tips for troubleshooting the next time.