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/.

umount both drives

then copy mbr

dd if=/dev/hdx of=/dev/hdx bs=512 count=1
 

I recalled this from memory but I don''t think I left anything out, but your mileage may very, at this point you could replace your orginal with your backup and it should boot just fine.
I use this method to copy/resize new virtual images and works quite good and fast.