I know the show wants us to believe that Dipper had absolutely no leads aside from McGucket from Journal 3 and The Bunker, but I beg to differ.
I was checking out a few entries from the book. Ford specifically mentions renting a cabin from Boyish Dan at some point...I don't think it'd be too hard for Dipper to connect the dots that's Manly Dan lol. And these were specifically the pages on classifying ghosts which we KNOW Dipper read in the Northwest Mansion episode so he definitely saw that and never thought to talk to Wendy's dad lmao.
And as much as Ford didn't really connect with his neighbors before the portal incident, he details quite a few interactions and mentions visiting several locations that the kids could have easily followed up on.
But at the end of the day, Dipper was too secretive about the journal to ever flat-out ask the townspeople about a scientist in the woods. Otherwise I think he would have solved the mystery halfway through season one, or at least he'd think he did because he would have believed Stan was the author. I'm not too sure if he'd confront his uncle about it, though. At least not right away.