Using FTP to grab all the files doesn't strike me as a good idea... all symlinks will become normal files, /dev and /proc will be a mess.

How about tar or cpio? Mount both drives in the empeg and copy all the files:

cd /
tar cf - /dir1 /dir2 /dir3 | (cd /newdrive; tar xvf -)

My empeg's in the car right now and I don't recall all the directories in root that would need to be copied. Would be easier if tar had a -xdev option like find does, but AFAIK, it doesn't.