Or you could boot up with knoppix or some other livecd so the filesystem is not in use and mount both drives and do a:
mkdir /mnt/org mount /dev/hdx /mnt/org mkdir /mnt/bckup mount /dev/hdx /mnt/bckup
cp -af /mnt/org/* /mnt/bckup/.
Won't this command choke if there are too many files? I think I have run into that before.
Matt
umount both drives
then copy mbr
dd if=/dev/hdx of=/dev/hdx bs=512 count=1