FANTASTIC NEWS! I've fixed the errors. Some of the triggers were broken, and deleting them removed the errors. If anyone finds similar problems, go to the story folder of your mod and check out the "log" text file. I scrolled down until I found the errors which seemed to be clustering around teleport and patrol triggers. If only the error message had told me that the errors would be displayed in the log file, I could've solved this months ago >.<
Anyway, less fantastic news is that I've probably lost my level designer. Also, I'm working on the mod in my signature right now, so I want to finish that first (and I'll be able to apply those learned skills and changes to my mod anyway).
Of Doves and Demons really is insanely ambitious and if it does get finished, it's going to be way pared down compared to what I had originally imagined. I might only finish the first town, but that alone is going to take me a while to flesh out because it's going to have a number of quests.
Ultimately, this might be more of a passive, dialog heavy kind of mod than I had first hoped for. But that depends on how good at scripting I get and my own patience. Thanks for the support, though. Without your inquiry, I probably would not have investigated again (or at least done so much later).