@Prince_Charmless, you have to see this!
But yeah, I ship DipperXWendy. Like, really hardcore. The age difference means NOTHING to me, considering that something could happen to make the kids older, kinda like what happened to Lloyd in Ninjago. It's a possibility, maybe Dipper and Mabel are magically turned 3 years older, and as a side-effect to that, DipperXWendy becomes canon. I mean, in the newest episode with the time travel, it's clear Wendy likes Dipper too, but it appears that the age difference is the only thing holding them back, so I hope for the sake of the ship, either Dipper gets older, Wendy gets younger, or Dipper and Mabel keep coming back to Gravity Falls every year, and eventually Dipper and Wendy are closer in size and the age difference becomes less noticeable. As for the part with Dipper not living in Gravity Falls most of the time, the two of them could keep in touch via the interwebz, and a few trips during the summer, winter, spring, and other breaks in between. As for the journals, my theory is that it's just the guy from that one episode, except he's not actually a shape-shifter.