Help! iCloud Deleted My Mailbox Folders in Mavericks

So I recently upgraded to Mavericks. I realized that when I went to System Preferences > iCloud, (which had me log in through Safari i.e. www.icloud.com) most of the items like: Mail, Contacts, Calender, Notes, Safari, Documents and Data, and Keychain, were checked. What wasn't checked was Find My iPhone. On my iPhone the only thing checked is my Find My iPhone, since I have had nothing but HUGE HEADACHES with iCloud. I presummed that my Desktop or Account would have reflected the same checked boxes as on my iPhone.

Problem: So I decided to uncheck Mail on the iCloud.com. I first viewed Mail (on iCloud.com) and it didn't reflect my Mail in messages or folders as I have it set up on my Desktop. None of my emails, folders, etc. were displayed, only two iCloud welcome emails. So when I unchecked Mail I got a pop up that said: "If you stop using iCloud for Mail, Mail stored in iCloud will be deleted from this Mac. Your Mail will still be available on other devices using iCloud." When I pressed OK I noticed that all of the sudden all my Folders in Mail vanished, though my Inbox emails, Trash emails, etc., remained. I tried to recheck Mail box in iCloud and it didn't change anything back.

I then tried to recover my folders from Time Machine. Time Machine stated: "Click Restore to recover your Inbox on Gmail. Or select another Mailbox or specific messages to recover". However the "Restore" button is greyed out and Time Machine won't let me go back to a previous backup. Actually Time Machine won't let me do ANYTHING in Mail. I can only hit the cancel button.

Lastly, I found that my files still exist in Library > Mail > V2 > Mailboxes > Private Folders (the main folder I created for Mail). It has all the subfolders listed under Private Folders just how I used to have it and now want to try to get it back like before, but I don't know how to restore them...

Any help would be very appreciated!

Christian