The reason that the engine has two numbers is that the smokebox front never appears in the movie, only the cab, wheels and tender.
The combination car is a reconstruction built on a flat car frame for easier maintainence. Reader also has two additional passenger cars built on flat car frames.
The train appears both in the early part of the movie (set in 1872) and at the end (set in 1902).
The Wye was not used for the picture, only the maintainence of way siding and the passing siding.
UP signal crews removed the crossing signals for the main street in Granger so that they would not appear in the movie.
It was interesting to see all of the passengers on the daily Texas Eagle craning their necks and taking pictures as Amtrak rolled through under a slow order on the days that they were filming.