While we can use "it" to refer to a train in certain contexts, there's no pronoun specifically designed for trains.
For example:
* "The train is late." ("It" is a general pronoun used to refer to the train.)
If you need to avoid repetition of "train," you could use a descriptive phrase instead:
* "The steel horse is late."
* "The iron giant is delayed."
These phrases are metaphorical and add a touch of imagery to your writing.