Your example doesn't contain the phrasal verb "take up" but rather up applies to a direction of travel. It just so happens that the context of the statement is very similar to the phrasal verb. In this context: Taken = to take a vehicle as a form of taxi (eg., "I took a taxi.") It = Refers to the train, the object of the verb. (eg., "I took a plane. -It- had very comfortable seats.) Up = the direction in which is traveled, this is used occasionally in reference to the direction on a map in which one would appear to travel. In this case, the subject is likely American and thus travels "up" to Canada.

Hello SonGoku, "take up" as a phrasal verb has got many meanings. One of those meanings: If you take up something such as a task or a story, you begin doing it after it has been interrupted or after someone else has begun it. So it could mean here that he used to take the train a lot when he was little and in his youth , then took it up and began doing it again as an adult after having stopped it for years. Another meaning : If you take so up an activity or a subject, you become interested in it and spend time doing it, either as a hobby or as a career. So it could also mean here ,that he became interested in traveling on trains and spent some times traveling as a hobby he likes to do.

Another way of writing the third sentence is, "And I've taken the train up to Canada a few times," meaning he's traveled on the train. "Take up" also means "to begin", as in "I've taken up guitar playing as a hobby," but that is not the meaning here.