Keychain problems

I've been having a lot of problems with my keychain folder. It was duplicating the metadata.keychain file over and over until it had filled about 300gb of space on my HD. I fixed that problem but now keychain and mail isnt working right. Keychain wont accept any new passwords and mail wont either. Mail wont save or approve any passwords for my accounts even if I put them in under preferences. I get this when I run keychain first aid. 
Repair started
Checking keychain configuration for jb (user ID=501)
Home directory is /Users/username
Checked login keychain
Checked password for ~/Library/Keychains/login.keychain
Checked settings for ~/Library/Keychains/login.keychain
Checked default keychain
Default keychain is set to ~/Library/Keychains/metadata.keychain (instead of ~/Library/Keychains/login.keychain)
Unable to update /Users/username/Library/Preferences/com.apple.security.plist
Warning: to use the passwords stored in “metadata.keychain”, you will be required to manually unlock that keychain. If this is not what you want, use the Keychain Access application to copy those items into “username”, or delete the “metadata.keychain” keychain.
Checked keychain search list
Checked contents of ~/Library/Keychains/login.keychain
Warning: some problems were not fixed
Repair failed
I tried deleting the metadate.keychain but it doesnt change anything and it just restores after I log out and back in. Also when I log in, applications that were not running when I logged out are opening. Some of them I havent used in months. None of the applications that are opening at startup are in the list of login items. I reset the pram and ran disk utility and the permissions came back fine. 

Triple-click anywhere in the line below to select it:
ls -@Oaeln L*/K*
Copy the selected text to the Clipboard (command-C).
Launch the Terminal application in any of the following ways:
• Enter the first few letters of its name into a Spotlight search. Select it in the results (it should be at the top.)
• In the Finder, select Go > Utilities from the menu bar, or press the key combination shift-command-U. The application is in the folder that opens.
• Open LaunchPad. Click Utilities, then Terminal in the icon grid.
Paste into the Terminal window (command-V).
Post any lines of output that appear below what you entered — the text, please, not a screenshot.

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