Being addicted to railroad songs, I have done some reading and offer the following ideas.

It this song, "modern combination" refers to it being a freight/passenger combo. Disagree on folk etymology from "hobo's accommodation" but would accept it if given documentation, like earlier version done the other way.

No changes--I agree with the suggestion made. The train is an express or a "limited," making few stops. Ergo it does not stop at all possible change points.

"Riding thru the jungle" if it's in your version refers to "hobo jungle," term for a hang-out where bums built shacks of tarpaper and scrap wood. Otherwise conjures up a strange unintended Disneyland-like vision.

Line I always wondered about was the second one, which I have possibly mangled or maundygreened somehow: "Across the wide Atlantic to the great Pacific shore, from the queen of flowing rivers to the south belle by the door." (?) Figurative ref to the Mississippi flowing past New Orleans, the "south belle by the door?"

Also apropos of nothing, used to start last verse, "Here's to Boston Blackie, may his name forever stand, and will he be remembered through the whole of all the land." Friend named Alabama Southard told me it should be, "Here's to Daddy Claxton, may his name forever stand, And will he be remembered through the whole of Alabam'." Sung it that way ever since.

CC