How should I make sure the user identity associated with application pool running SPLMS web application has farm admin rights?

You can do this using either way:

  1. In the ISS settings, application pool settings, identity.
  2. In Central Administration in Service accounts you can look up what account is used for a web application.

When you find the account, make sure it's included into the farm administration group. 

If it's not add it to the farm administration group, and restart the SharePoint services and IIS.

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