I have been following this thread, trying to figure out what the problem is. I can download PDF (and other) files , with no troubles.
I am running ArcaOS 5.0.3, with Firefox 45.9.0. Firefox has ZERO add-ons (which is probably the key to success), and one plugin (Open H264...), that says it "will be installed shortly", but never does. It seems that it isn't needed anyway.
When I click on a PDF file, it opens for read, in a new window in Firefox. At the top of the window, there are buttons, and one of them is Download (sometimes, you need to expand the menu selections, with the far right button, to see the Download button). After it is downloaded, I use Lucide to read/print/edit (when it has edit fields) the PDF file.
You can also RMB on the download link, and select "Save Link As...", without opening it for read (normal download procedure).
Have I missed something? What else do you want to do?