Ok, I find all this discussion very odd: I have no problem opening PDFs in PDF2Go from SD card, USB, or even Dropbox. I use either Astro File Manager, ES file Explorer or Droidbox to navigate to the file, and when I click on the file it asks me whether to open with Library or PDF2Go. If I chose PDF2Go the file opens just fine.
I do have some issue navigating the directory structure from inside PDF2Go (crashes when i go up to root folder), but I seem to be stuck in the /extsdcard folder, which is the SD card, not the internal storage. So it's the opposite problem of what others seem to be having. Not sure how my PDF2Go ended up there.