The tune Homer plays on the harmonica and Clementine sings is "Lorena" (1857), a very popular song with Civil War soldiers of both armies.
Wagon Train Tracker: The episode begins in the town of "Cinnabar," entirely fictional. Reference is made to the train approaching "Saunders." Saunders County, Nebraska is west of Omaha, though the county seat is Wahoo. So, consistent with last episode, the train must be moving from southeast to east central Nebraska, somewhat parallel to the Oregon Trail.