Our site currently has 9 PDFs - if you click them they open in a new window or you can right click and download. The problem is the PDFs content is also wrote up on the site under information articles. To make things worse, the sames PDFs are also on another site -- This means the content is in 3 places as far as Google is concerned: Site 1's articles and PDFs and site 2's PDFs. Should I de-index the PDFs altogether, can I make it so that Google treats the site articles as the main source of that content?
Well... This could cause the problem. I am really curious why did you use the SAME information on all of them?
Why not just host them on let's say Dropbox or any file sharing website and provide link on the website for download?