Complex sentence: The only differences are as follows: at the New York terminus, it runs to Penn Station; on the Chicago end, it switches to the former Pennsylvania Railroad's Pittsburgh, Fort Wayne and Chicago Railway at Whiting, Indiana, running into Union Station.
Split into simpler sentences: The only differences are as follows: at the New York terminus, it runs to Penn Station. At Chicago, it switches to the former Pennsylvania Railroad's Pittsburgh, Fort Wayne and Chicago Railway at Whiting, Indiana, terminating at Union Station.