Honestly.. Site A is a Cash Cow that does not need SEO. I would love to clean it up, but there are external forces preventing that at the moment. These forces are not technical.
Site B is in the same industry as A, but with a different model and user. Both sites are pertient.
Let me simplify this question....
1.Can duplicate content effect more than just the root domain and spread across to other websites on the same IP range? and WHOIS?
2. Moreover does any SEO need to worry about what their clients are doing on sites that are out of their control (assuming no blackhat techniques)?