As each website are totally indepedent, that mean that you can use the "custom modules" to put specific header for each website (master and/or slave sites).
Concerning the Google Analytic, you can use our free multisites google analytic module available in our free download
www.jms2win.com/free-download/doc_downlo...tes-google-analytics
With this module, you can give specific GA track id for each website.
This will avoid you to modify the themes (templates) or CSS to include such GA code and also this will allow you to have specific GA track id event when you are using the same themes (template) between websites.
We are using this module for jms2win.com and faq2win.com that are slave sites.