I have never really used pdf files with evernote. Not that I wouldn;t, I just haven’t gotten around to it yet — great tutorial, Evan! I am sure I will be reading it again when the time comes.
One major issue I have always had with evernote is their clipping functionality. I find it counter-intuitive at times and best suited only to web clips, and that via plugin. Using the clipping shortcut from the desktop app has only lead to frustration and, as such, I have kept One Note installed just for their clipping feature (often, I need to clip something quickly to copy it into photoshop and asimple windows+s button combo brings up an overlay that allows me to drag over anything visible on my screen).
Oh, and continuing the sidenotes here, Evan, you may want to test out Intense Debate. Many people seem to prefer it over DIsqus.