Instead of using a PDF viewer, you could outsource the search job to Recoll, Linux' most powerful desktop search engine. Recoll creates a full-text index of your PDF files (and many other file types), which you can then search through as if you were using Google. It's capable of searching through individual files and showing all search results in a neat overview.
You can get the newest release from the developer's official PPA by typing:
sudo add-apt-repository ppa:recoll-backports/recoll-1.15-on && apt-get update && apt-get install recoll
Unfortunately there's still no tutorial on how to use Recoll here on Askubuntu (something I hope to do in the future), but the official documentation is very detailed.
After you've set up Recoll you can search through a specific document by setting the search mode to query language and wording your search like this:
You can access the result overview of a specific document by clicking on Snippets. If you have
evince installed (the standard PDF viewer Ubuntu ships with), clicking on the page number will direct you to the corresponding page and pass the search term to
evince's inbuilt search. You can then highlight the search term by hitting CTRL + F in
Recoll's advantage over the inbuilt search in PDF viewers like
acroread is that it operates with a pregenerated Index. This makes searching for a term almost instant, even when working with thousands of documents.