Do I believe a virus caused a copy & paste of all of your system drive to fail? Very unlikely
First off on the system drive there are many hidden and protected folders. Second, W7 uses pointers so that a folder can appear to be under another folder even when it is not (this is what makes your W7 libraries work) but a simple copy would just follow down the path creating copies of the files/folders where W7 pretends they are as well, as where they really are, giving you duplicates. Third, W7 actually has some of these pointers pointing back to the parent directory which causes an infinite loop. And fourth, there used to be and, I believe still is, a limit of 254/255? characters in the total path length which means if you are starting at the root directory with a copy you may not be able to reach the deepest buried files/folders.
Basically if you want an exact copy of your system drive you "clone" it, not copy it. There is lots of cloning software available. Our
Freeware DB includes links to Macrium Reflect Free or if you have a WD or Seagate drive there is software listed that works only with those drives. Paid versions are also available with more features but the free version is usually adequate for most individuals to get a nice cloned back-up.