unable to download pdf files from websites

Far as I know the problem isn't on Apple's end. I'm download PDF files with no problem. But I've experienced what you are in the past and I think you were on the right track when you suspected Adobe. In the main Library folder (not the one in your personal directory) there's a folder called Internet Plugins. Look inside for a file called AdobePDFViewer and delete it. If I remember properly, you force Adobe Reader to install a new one by just starting Reader and it will ask if you want to install the PDF reader. Or, you might want to look at this plugin which, in my opinion, beats Adobe's plugin hands down.

What happens if you right click or control click on the file? Any options to download?

That's not good. Let's hope some one else come's along with an idea. I have no others. I can suggest that you create a new user account and see what happens but if you can download PDFs I'm totally flummoxed on what is causing your problem. But if your problem persists that would mean there's something wrong with the OS or Safari itself.

Two more thoughts. 1) did you restart Safari before downloading a PDF? 2) do you happen to have SpeedDownload or another YazSoft download program installed? That might be interferring with the download.

Thank you dwd that solved my problem I was able to download my pdf properly after that! =)