How to repair ~/Library permissions?
It's possible that the Reset Home Directory Permissions and ACLs option in the resetpassword tool will correct those permissions for you, though I'm unsure how 'deep' into your home directory it will reset.

This blog post gives the steps for Lion, which appear to be the same in Yosemite (Note: that last link details instructions for resetting a password, which is obviously not what you are doing here, which is why I linked to the Lion instructions. However, the same tool is used in each process):


  
  Restart, and before you hear the chime, hold down the Command and R keys.
  You’ll be at the Repair Utilities screen. Click the Utilities item in the Menu Bar, then click Terminal.
  In the Terminal window, type resetpassword and hit Return.
  The password reset utility window launches, but you’re not going to reset the password. Instead, click on icon for your Mac’s hard drive
  at the top. From the dropdown below it, select the user account where
  you’re having issues.
  At the bottom of the window, you’ll see an area labeled Reset Home Directory Permissions and ACLs. Click the Reset button there.
  
  
  The reset process takes just a couple of minutes. When it’s done, exit
  the programs you’ve opened and restart your Mac.