Ubuntu 9.10: Add Full Disk Encryption to Existing Installation Without Losing OS Customizations and Data

Hi,

I am relatively new to Linux. I recently installed Ubuntu 9.10, and at the time, I was unaware of the alternative install cd and its option for whole disk encryption. At this point, I have customized my system enough that I would really like to avoid having to simply reinstall from the alternative install CD and start from scratch. I would like some way to add full disk encryption while preserving my existing system.

I have read the relevant HOWTOs and other available documentation on the web. My conclusion is that the easiest way to get the best possible full disk encryption setup is to use the alternative install cd. In case something goes wrong, I have performed an image backup of all of my partitions using Clonezilla.

1) Regarding the encryption part of this, do you agree that the alternative install cd is the best and/or easiest method to reach my goal?
2) My guess at how to do this would be to use some file-level backup program to backup everything, then install a fresh installation with full disk encryption from the alt. install cd, then restore all of the files. Is this the best way to go about it?
3) I have some questions about how this works in Linux:
When I boot into the fresh OS that I just installed from the alt. cd., I will need to install the backup program and then restore the files. I am coming from a Windows background. In Linux, can you simply restore all of the files which constitute not just your data, but your original OS install, and write them over the current OS install that while it is running, then just reboot and your system will be identical to how it was when you backed it up?
4) Would you please recommend a suitable backup program?

Thanks so much for your help.