Both StoreFront servers are Server 2012R2 fresh install and fully updated.
Clean install of SF 3.13 completed successfully on both servers.

• Log Name: Citrix Delivery Services
• Source: Citrix Configuration Replication Service
• Level: Error
• Description: An error occurred running the command: 'Add-DSFeatureInstances' Physical path: C:\inetpub\wwwroot\Citrix\NTCWeb associated with Virtual path: /Citrix/NTCWeb is already in use.

1. Delete the StoreWeb folder from 2nd Server from path C:\inetpub\wwwroot\Citrix 
2. Try replication