I thought your problem was just settings(and what about your desktop is different? It's in the home folder, so unless you've installed a theme using emerald or something similar it should be the same).
will make a list of all aplications you have installed, when that's a complete(should take a couple of seconds max) use
dpkg --get-selections > pkg.list
to install them on the new HD. I think that's almost everything...
sudo apt-get update
sudo dpkg --set-selections < pkg.list
sudo apt-get -u dselect-upgrade