In this step we copy various directories from source machine's disk (image) to the target machine disk (image) after removing the destination directories. However, in order to do this we need to have both machines turned off! Or more correctly, they must not be using their disks.
Before going any further, ensure you have a backup of the source computer. Human nature being what it is, (i.e. a set of rules we all obey) says that you shall get confused, and you'll copy the target computer over source and lose everything.... but you'll have the backup right?
The cloning challenge then, is to access both disks at once, effectively from a third machine. Many possibilities present themselves.
Here at WT we have a special VM who's role in life is to have lots of "virtual" disks attached to it. You could also do this by attaching physical disks to a third machine. You could also boot the both machine from a linux rescue disk and then copy files over the network. All of these techniques work and have been used at one time or another.
... to be continued.