The Big Bad isn't Bill Cipher...
It's Him. The fic regularly mentions them having a multilayered voice, as though a man and woman were talking at the same time, a humanoid form, and black boots.- Mike and Stan do indeed call him "Him" when discussing him with the kids, mentioning that he never told them his real name.
Wendy's BFS belonged to The Scotsman.
It's described as having glowing runes, and the Corduroy's in this story are stated to be of Scottish descent. After she left Blythe Hollow, Lydia married and had a daughter.
This daughter's name? Sam Manson. Gideon will tempt Dipper into his side.
The Ford seen at the end of Chapter 18 isn't the real Ford.
It's a doppelgänger conjured by Gideon and/or Him to manipulate Dipper into doing their evil deeds. Tucker is related to the slave family Walker killed
His expression turned stern when explaining this.