Using Chrome extensions on PDF Files
Solution 1:
open your PDF file`s using this website: http://pdfviewer.softgateon.net/ (or similar website), then you can use Google Dictionary extensions
Solution 2:
try using mac osx instead.... I guess there's no way easy to solve this, except altering chrome's source code to replace the adobe pdf plugin.
"Due to technical restrictions, you cannot select text and translate it by a shortcut in PDF files in any browser. Unfortunately, we can do nothing with this. However, in Google Chrome you can select text and translate it instantly from the context menu." ----matetranslate.com
Solution 3:
I use Mendeley website for reading and managing my PDF files. In this way, the google-translate extension pop-up works on the text properly.
However, I understand that this is not an ideal solution as you need to register on the mentioned website and upload your PDF file which could be done by the Chrome browser itself ideally.