After a bit of thought, I now think that Stan might be the author of the three mysterious books.
Short to the point, and I can be wrong (it's an opinion), even though we haven't seen the first, Stan may possess it. The location where Dipper found Book 3 is highly suspicious. Maybe Stan, hypothetically being the author, never got to finish it, and expected his nephew/niece to finish unlocking the town's secrets. But, it could be too "unsettling" if Stan bluntly told them that there IS something strange about the town, thus he ignores it.
Also, maybe Gideon's rivalry with Stan is somehow connected with the town's "color," since Gideon does use Book 2 for revenge against the Pines family.