The autounattend.xml files are not completely unattended unless you set them that way. So yes, I'm saying manually set your partitions.
The folders you want to backup(get a bigger external drive for this, 500+GB) are as follows;
C:\Program Files
C:\Program Files (x86)
C:\ProgramData
C:\Users
As well as anything you have in custom folders elsewhere.
I would highly recommend you use a file copying utility to do the files transfers. Example;
www.roadkil.net
Specifically;
roadkil.net
However, drag&drop will work. Unstoppable Copier is a bit faster, customizable and more informative.