I try to simulate your setup and found some interesting details.
If you need to create web application on a remote server, you first need to create a virtual directory on remote server and mapped it to a physical directory so it should look like http://remoteservername/dirname
In next step while creating the web application project , studio will ask you for the server path name. Provide http://remoteservername/dirname
there and it should work then.
Hope this will work for you.