Stream3 is published with video from Stream1 and audio from Stream2
The error you are getting is stream not found, suggesting that ffmpeg cannot handle appInstances. It is treating instance/stream as the stream name.
You could remap the appInstance that ffmpeg is connecting to by using IVHostNotify.onVHostClientConnect in a custom VHostListener. This method is called before the rtmp client is connected to the application so it can be remapped to a different application or appInstance. The problem is that rtmp streaming is a 2 part process and at this point, you will not have the stream name part of the url so wont know which appInstance is actually being requested. Once the connection is made, you would also have to remap the stream name to the correct name using IMediaStreamNameAliasProvider2.resolvePlayAlias(IApplicationInstance appInstance, String name, IClient client) in a custom module.