Some Windows and other settings can be saved from using the Files and Settings transfer wizard. However, if you are transferring from Office 03 or above, it does not grab these reg entries (last I tried). To transfer these I needed to script it in the files for the wizard (in the USPTO directory I believe).
Anyway, for other applications, you would need to script it as well, or you can purchase a 3rd party tool. However, I doubt that these 3rd party tools would get everything as well, and may require scripting.
Part 2 -- you can add them to the install, however you would need to download them again and then configure and make a new install disk after slipstreaming the updates