When trying to save a PDF file I have it set to use my PDF viewer but once I use it, it switches back to "Save PDF" for the next time? How do I stop this?

The action that you see in "Tools > Options > Applications" are tied to a specific MIME (content) type. *http://kb.mozillazine.org/File_types_and_download_actions Firefox only support the built-in PDF Viewer for the application/pdf MIME type (likely the second entry: Portable Document Format (PDF)), so if the server sends such a file with a different MIME type then you may have created another entry like the first entry Portable Document Format.