I confirmed that when I duplicate a fresh copy of the index.html file, it doesn't give me the StoryInit error, so that must be something I did even if I can't find it. Whoops! (Edit: I figured it out... I put quotes inside the quotes to denote a nickname, like an absolute casual...)
What's interesting is that while opening the index.html directly doesn't give me the config error, duplicating it (to give it a fresh IFID) and then marking a starting point (can't Publish to File without a starting point) and then opening that file gives me the config error. So it must be one of those two actions that's messing it up, right?
Either way, thanks for replying!