Hyserski
You shouldn't use a backup INCLUDING system files (those that start with a dot . ) as they most likely screw up a fresh install (I know, it hapened to me several times).
They are created a-fresh when you install a-fresh.
If you use something like rsync (or Grsync, which is the same app plus a GUI for it) you need to tick all boxes that keep the original permissions. There's no need to paste something from an old backup into a freshly installed system that hasn't got the appropriate directory and files permissions as you won't have access to your backup.
What I wrote in another thread:
In Grsync I had to check/activate the following boxes:
preserve modification times
preserve owner
preserve permissions
preserve group
no space-splitting; only wildcard special-chars
run as root
I also changed permissions for all my directories and files to 777 as I am the only user of my computer.
Worked.