Since it was established that the rift was caused by the portal, something that was built by salvaging alien tech, and that the rift allowed Bill's weirdness a gateway into our dimension, my theory was always that the hyperdrive tech on the alien spaceship ended up opening a rift or two when it was damaged in the crash and that this was what started the initial wave of weirdness in Gravity Falls.
Shortly after the crash, a shaman from the local indian tribe is sent to investigate the sudden appearance of all these strange spirits and wanders into the crash. The aliens are all pretty much dead at this point, except for maybe one that helps him to seal the rift later, but he does end up stumbling across the rift responsible for all his tribe's current trouble. The Shaman ends up taking a look inside of one of the rifts, meets Bill, and like McGucket is forever changed by the experience. Unlike Ford, he realizes that Bill is no good from the start, seals the rifts using the alien adhesive, makes the cipher wheel as a means to defeat him, and as a last line of defense, puts a defensive barrier around the town to keep all weirdness sealed within.
Anyways, that's my crappy fan fic idea.