Several weeks ago we started seeing some pretty scary errors showing up on the main system disk for our Blackboard server. We had an extra server hanging around, so we decided to move all the data off the failing disk and onto our spare server. The only question was how to make the new server as close to a perfect copy of the old one as possible. Simply restoring all the filesystems failed for a variety of reasons, mostly related to GRUB and the kernel, so I had to find a way of excluding only the files and directories that were tied to the specific model of server.
To do this, I started by installing a minimal copy of RHEL 4, making sure to lay the filesystems out in exactly the same way as they were on the old server. I then went through several experiments, leaving just the bare minimum files and directories required for the hardware and booting, but formatting all other filesystems and restoring the data from our old server. In the end, the below process resulted in system that worked perfectly, and very closely mirrored the original server.