Before you do that, I would install Systemback.
http://sourceforge.net/projects/systemback/Installation:
sudo add-apt-repository ppa:nemh/systemback
sudo apt-get update
sudo apt-get install systemback
Using systemback, create an ISO of your current OS - you could possibly use it later.
I havent played with Mint for some time, I found this:
http://community.linuxmint.com/tutorial/view/344Here is how I would guess you can do it.
Use systemback, create a bootable ISO (keep in mind, if you have installed a kernel that didnt come originally with your OS, it most likely wont have AUFS module installed, which means it wont boot in live). So make sure your using the kernel that came from your source repo.
After you have your ISO, boot it, try to setup full disk encryption and then use systemback to install the OS.
If you dont want to try that. Then atleast compress your ~/.config, most customization's are there. Might as well compress /usr/share/themes and /usr/share/icons too.