Originally Posted by count0
Now that I am going through and correcting the metatdata, the folder structure is still incorrect.
I find that statement to be very strange because it begs the question: What were you expecting?
If you entered the correct title and author then the book is stored as:
<path to calibre library>/<author>/<title>/<title.extension>
This is both normal and correct assuming you're talking about a computer not an ereader (many of which have their own file systems for storing ebooks). Calibre has to control the organization of your library in a specific structure otherwise it cannot know where files are located. Calibre uses the exact info entered per book to create the structure used to store your books.
If you are not seeing your calibre library of books arranged in this manner than something is wrong.