Is there a way you can take advantage of iframes? Google is able to just look at the source of an iframe, but it can't crawl an iframe directly into the parent page, as far as I know. So, the iframe source should be noindex.
Your web server contains a configuration file with a configuration that directs traffic from certain sources to pages with the suspicious script. If you're using apache, start with the .htaccess files in your document root folder and every folder recursively within it. Look for any lines containing "user_agent" or "remote_addr" or even google or other ...
You need to make sure that both servers have the exact same document root folder defined in the configuration files. In a fresh install of apache, look at httpd.conf and find contents similar to this: # # DocumentRoot: The directory out of which you will serve your # documents. By default, all requests are taken from this directory, but # symbolic links and ...
Google has a spec for AJAX (SPA) applications, https://developers.google.com/webmasters/ajax-crawling/docs/specification. basically you need to provide the server the same content, but by using classic web site (request-response) technology. I call it a core site.
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