So, I try to stick with these concerns in the "land of reasonable". With every security issue there is a balance of secure v.s. safe. For example, you could buy a laptop, read one PDF loaded from the web mail side of your email provider, re type any content you need on a "main computer" then destroy the laptop starting all over again with a new laptop. That would be pretty secure. Also costly, and a giant pain.
So back to a "reasonable" approach.
First, use Linux and a up to date PDF reader. By doing so you have really reduced your exposure. There are not as many viruses written for Linux as there are for windows. That alone will protect you quite a bit. The viruses that do work on Linux are more complicated to implement. Again reducing your exposure.
Next use a Virtual machine that supports snap-shotting. The idea is that you setup your Linux OS inside a virtual machine host (like VirtualBox) get it all setup then, "Snapshot" the state.
You can then do all your "risky" work inside the virtual machine. Using isolation options, I don't know of any virus that can "escape" the virtual machine and get to the host machine (doesn't mean they're not out there, just means it's more rare, and more complicated for the attacker).
At the end of the day, or any time during the day when you think you have gotten a virus, then you "revert" the machine to the previous snapshot. All the changes and data that "happened" after your snapshot are undone, including any work, viruses, etc.
During the day, you can open a PDF, scan it with ClamAV (or the like), copy and paste what you need, or what ever you need to do with the PDF files, so long as your Virtual Machine exists in isolation. That means that you don't give the virtual machine access to the host machine. You use something like email to transfer the files. Maybe FTP between the host and the virtual machine. Something, but not direct integration. Not dropbox either. Something where if you're going to transfer the file, then you're only going to transfer that one file after you're pretty sure it's safe. If you're using a Linux host and a Linux guest then scp is a great choice.
This gives you a "pretty secure", disposable environment, to check your questionable PDFs out, with the ability to "undo" damage that may happen, without having to really change much in your work flow.
Virtual machine hosts and guests can be almost any OS including Windows. Keep in mind that if you have a Linux guest and a Windows host the Linux virtual machine may not even be susceptible to a virus that is in the PDF that a Windows machine will be susceptible to. Scanning with an anti-virus scanner is important, no matter the OS combo in use.