I am using Nginx as a proxy behind Apache
I have setup my network to use sub-folders NOT sub-domains
I placed the above code into my .htaccess file and the sub-site URLS works on the front end. However, when I try to access the admin URL for a sub-site it throws a 404 error.
More guidance is...
I think what you need is the plugin called NS Cloner Pro. The lite version of NS cloner is in the WP repository, but I am not entire sure it does everything you are looking for but try it first.
There are also other Multisite cloning plugins available, just Google it