Attempting to configure SQL Merge Replication when Active Roles is configured to connect to SQL using a custom port fails with the error:
A network-related or instance-specific error occurred while establishing a connection to SQL Server. The server was not found or was not accessible. Verify that the instance name is correct and that SQL Server is configured to allow remote connections. (provider: Named Pipes Provider. error: 40 - Could not open a connection to SQL Server)
This is due to a limitation in Microsoft SQL. Merge Replication cannot be configured when the connection string contains custom ports.
After these steps have been performed on all Active Roles Administration Service nodes, promote and add subscribers in the Active Roles Console as per normal.