Who wrote the journals? The biggest contender seems to be Stanley Pines.
In Tourist Trapped, we see the monocle in journal #3. Apparently, the monocle is not in either of the other two. The monocle could have some significance as to who wrote the journals, or it could be nothing.
About a minute later, we hear Dipper saying "like the guy who was writing it mysteriously disappeared." This may seem like just an observation, but I think it was a hint that the guy who was writing the journal did mysteriously disappear. It points to the evidence that the journals were written by Stanley Pines.
Scaryoke and Into the Bunker confirm that the author, at least at one point, had six fingers. Scaryoke also confirms that the author wrote in invisible ink, but Stanford did not know about it. This eliminates him as the sole author of the journals.
Obviously, Society of the Blind Eye eliminates McGucket as the sole author, but confirms that they were working together.
My personal theory is that it was Stanley, but he was working in conjunction with Stanford and Old Man McGucket. See here for more on that theory.
Whoever the author is, we didn't know much about him until Into the Bunker. Clues dropped in that episode include:
A weapons cabinet. We know that the author was paranoid, so it makes fairly logical sense that he would be ready to defend himself.
A calendar of 1982. This is further evidence supporting the idea that the author disappeared in that year. Personally, I think the author was Stanley, and he disappeared into the portal on July 4, 1982. (Apparently that was also the date of some nuclear testing in Russia. Makes sense why he would build a nuclear fallout shelter.)
Several boxes of supplies, lasting until 2070. Interestingly, assuming the author disappeared in 1982, these supplies would last for 88 years after that. If the author was a grown man at that time, he would be over 100 years old by 2070. Either he was planning on living an awfully long time, or someone younger was with him. (We already know McGucket was with him, but he was a grown man too.)
A recently opened can of beans. It could have been the shape shifter, but I think the bunker is actually connected to Stan's lab. Maybe the author was hiding there up until he opened the portal.
The shape shifter. So now we know the author had a lot of experiments going. Does the "Experiment 210" label remind you of something? Maybe an "Experiment 73" label? He also drops a huge but vague hint at the end of the episode. "You think you're so clever, don't you, Dipper? But you have no idea what you're up against. You will never find the author! If you keep digging, you'll meet a fate worse than you can imagine. And this will be the last form you'll ever take!" It's not unlikely that the shape shifter meant for Dipper to be frozen forever in that position in Northwest Mansion Mystery, but I think it was the writers trying to fake us out.
