I would personally tarbar the site but thats me.
I dont rightly know what you mean by correct path.
They normally reside in the data directory
Keep in mind doing a fresh install you will still need to copy over the mysql database of the old install to properly have everything correct so your best bet would be to just tarball everything and put on the new site and then upgrade to 4.8.2 on the new site.
You can then redo your header footer and after everything is right with fresh code begin modifying again.