Installing Patches on MS SQL Server Tips
Continuing to troubleshoot I did a search for sql repair perf-mssql13.mssqlserver-sqlagtctr.dll being used by another process and found the following article: Knowledgebase article: File in use by another process
The repair continued after I applied the same advice to the file in question.
When repair completed I was not able to start the agent service. I did a search for the following from the &quot;Event Viewer&quot;: failed to initialize sql agent log (reason access is denied) and found the following article: MSSQLTIPS: SQL Server Agent Service Won't Start Due to Access Denied
What I found out: when SQL is installed, it places a security lockdown on the log directory. It changes owners and restricts access to only the agent service account. The DBA that installed the system used default settings to install SQL Server, and then changed the service accounts to domain accounts. In this case, I found it curious the Engine Service account had access to the directory, but not the Agent Log files.
Solution: Check the permissions on the Log Directory and look for errors regarding the files.

Rename the file from the error during repair.
Added the Agent Service Account permission to the log in question and log directory.