Take a close look at the symbol drawing Allen has, as well as the one in the photo given to him, and you'll notice a striking resemblance to the flux capacitor time circuit from the Back to the Future (1985) trilogy, which was also by Robert Zemeckis.
The farmhouse the woman and her children live on is the same one Fox Mulder lives at in The X Files: I Want to Believe (2008). This could possibly be a visual call out to the X-Files nature of the show.
The episode is loosely based on the Flatwoods monster case of September 12, 1952.
When the spy went into Dr. Hynek's home office , there was a yellow rotary phone, which wasn't available till later in the 50's when color was mass produced. It also looked too lightweight.