What an strange issue, it started to give another error about how it couldn't launch _skimmer. But after I ran the _skimmer application from the workflow folder manually (and of course, got an informational message about what the app does), all my hyperlinks now function as intended.
Good god, it even works perfectly with files managed with Devonthink (which makes sense I guess, since DT really just buries files in its own structure). This is friggin amazing.
Going to try to set up DrLulz's fork as well, each are definitely useful in different scenarios. With this, it's time to move from Onenote to Evernote, and can't wait to incorporate an iPad into the workflow eventually too.
Thanks again for your help and the script!