CLONER: Cloning from Main Site to subdomains

Hi there folks
My multisite network consists of MAIN SITE (toplevel) mydomain.com and 9 subdomains site-1.mydomain.com to site-9.mydomain.com;

I have installed cloner and see that I have "clone" options for every site in the network EXCEPT the main top-level site:
ie I can clone from site-1.mydomain.com to site-2.mydomain.com etc but not from mydomain;

A. What I NEED to do is clone:
1. the theme (I'm using Genesis framework + Child theme);
2. Most plug-ins;
3. Policy pages (Privacy, t&c, copyrights, contact, about etc)

B. Once done, I would like to SELECTIVELY clone some posts to various sites on a site-by-site basis.

Would appreciate some help on working round this...
Many thanks in advance
Regards
Harry