Before I used Rikaichan and back then you could use the extension with pdf files open with firefox as well. For some reason, now pdf files opened with firefox will not show the pop-up window. Can you fix this? Also, if you could make this work with epub files it would be awesome.

EDIT: Thanks a lot for clarifying this problem, I have edited my review as this is something that the extension itself cannot solve. I used the link that you provided, this opens some unrelated pdf file and from then I opened my own pdf file within the same window and the plugin now works as it did before. Can you please explain what's special about that pdf tab that makes the extension work?