What to write in application letter to address poor grades in Greek and Latin for classical archeology masters application?
As you stated a lot has changed since those unlucky days and you've achieved so many successes since then. IMO, write that you do not believe that the grade is a real indicator of your current status and as a proof of your claim you can reference your research and papers if it is available online.

Note: In case the professor of your archeology class would give you a recommendation letter it would be so valuable.