You are really worrying about nothing ... you and Vanguard did everything correctly and there is NOTHING to fix. You DID put the income on the Sch E on your personal return filed in your SS# as required by law. Stop trying to fix something that is not broken. NO ONE is wrong not even the IRS.
If you really want the income transcript for the EIN then fill in a 4506-T and request one although it is a waste of time IMHO ... https://www.irs.gov/forms-pubs/about-form-4506
