My login keychain cannot be found. I have Keychain access but no Keychain repair option. OS X El Capitan
The login keychain lives in ~/Library/Keychains/

First thing I'd do is see if Time Machine has a backup.  

There is no Repair Keychain function in El Capitan. According to Apple KB: About the security content of OS X El Capitan 10.11.2


  Impact: A malicious application may be able to masquerade as the
  Keychain Server. Description: An issue existed in how Keychain Access
  interacted with Keychain Agent. This issue was resolved by removing
  legacy functionality.


According to rumour, it never worked since 10.11 anyway.