why not use disk utility which clones block by block?
+1
I've been using Disk Utility's Restore literally for years. Block copy is also faster than file copy by a longshot.
To enable block copy in Disk Utility, check the "erase destination" option. This also requires you boot off a 3rd volume (the Leopard install DVD is easy, but any other bootable (up-to-date is best) volume with Disk Utility will work). The reason is block-copy needs to unmount both the source and destination volumes.
Many years ago I used Carbon Copy Cloner, but it was slow and problematic (perhaps that's been fixed, but I lost trust in the app). I haven't looked closly at SuperDuper - it looks like it does go through a sort of "pre-flight" for you by checking permissions and verifying the source volume. That's good, and necessary, but can also easily be done right in Disk Utility. I know a lot of members here use SuperDuper, but I personally don't see the need.
Here's a quick run-down on using Disk Utility: Check permissions while booted on the source volume, then boot to the "3rd" volume. Run Disk Utility, verify the source volume, then prepare the destination - GUID partition map, HFS+ journaled. Restore (check "erase destination"). Wait a bit (depends on interface type and volume size). Enjoy clone.
A block copy won't have any issues with file permissions or broken links, which looks to be the show stopper in the OP's backup attempt. Of course, if there is a problem like a broken link, it will be dutifully cloned.
One more thought: since the block copy erases the destination, it's good to setup a partition on the destination drive. For instance: Source drive is 160GB. You wouldn't want to erase the entire 1TB volume every time you wanted to clone. It's probably a good idea, though, to make the partition large enough to handle a future, larger drive (like a 320, for instance). Keep in mind the destination needs to be the same size or larger than the source.
(note: in the "prepare" part, above, once the destination drive has been partitioned with the GUID map, it doesn't need to be done again - in fact, doing so will erase ALL the partitions on the drive (that is, if you change the partition map type). You can adjust the size of and add/subtract partitions dynamically, but you can't change the partition map without affecting the entire drive.)
Some background info:
Disk Utility is a front end for ASR (Apple Software Restore)
from the ASR man page:
HISTORY
Apple Software Restore got its start as a field service restoration tool
used to reconfigure computers' software to 'factory' state. It later
became a more general software restore mechanism and software installa-
tion helper application for various Apple computer products. ASR has
been used in manufacturing processes and in shipping computers' System
Software Installers.
For Mac OS X, asr was rewritten as a command line tool for manufacturing
and professional customers. asr is the backend for the Mac OS X Software
Restore application that shipped on Macintosh computers as well as the
Scan and Restore functionality in Disk Utility.
