I am looking for a comprehensive health check list for the backup exec servers and also some runbooks or links to perform operational tasks.Best practices.
Known error codes.
Example:How to configure ndmp backups?
The most obvious healthcheck fail I can see for your request is get to Backup Exec 15 and off 2012 (as long as the BE 15 compatibility list still covers eveything in your environment) - BE 2012 is no longer subject to product updates and had some design issues that were resolved in later versions
Apart from the admin guide covering some of your points there is no single place to find things like error codes, and even the restore process depends on what you are restoring.
A google search for Backup Exec best practices will find a lot of info as these are also split into separate documents depending on what you are doing.
A google search for Backup Exec Blueprints will also bring up useful info (although for BE 2014 and 15 and not 2012)
Maybe you should consider some type of formal training as a starting point for the information you are trying to get.