I'm not 100% sure if the pdf problem started after the Adobe Flash Player download and trashing.
I now can't download pdf files on either Safari or Firefox. I believe I read somewhere that emptying software into the trash may not completely uninstall it, because hidden files may still be there, but I figured I'd free up space in Applications. Since it's the office computer I wasn't about to get rid of Applications just because I didn't use them, so I trashed Adobe Flash Player. It downloaded, but I got a message that I was running out of room in Applications, and I should start cleaning out files. Some websites advised downloading Adobe Flash Player, so I tried to do that. (Sometimes during my lunch break I'd watch little video clips on Firefox, because they wouldn't play on Safari.) I was still using Safari most of the time, and was able to download, view and print pdf files on Safari. For a time Firefox worked fine for the 'difficult' websites.
For example I was no longer able to access information about my IRA mutual funds, so I downloaded and installed Firefox back in April. Some websites began to not 'work' properly on Safari. I'm not tech savory, but I'll explain things as best I can.
I'm fairly certain the problem started before I tried to install software, but that may have aggravated the matter.