My simulation has two types of concurrent threads:
First, the Journey class represents a Passenger's movement through the stations in its journey. The passenger begins at its starting Station. If that Station has multiple Lines stopping at it, the Passenger decides which Line's Platform to wait at. When the Line arrives, it signals the Journey's on its platform to board the Line, and the Journey selects the appropriate Car in the Line to wait on. When the Line arrives at that Car's Station, the Line signals the Journey to exit the train and wait on the Platform, and the cycle continues.
Second, the Line class represents a Train's movement through its stations. Each Line begins by acquiring the lock on its starting Station. Then, when it attempts to move to its next Station, it waits to acquire the lock on the next Station before moving. This way, when the Line moves, it has a lock both on the Station it is leaving and on the station it is entering. After the Line moves, it notifies the Journeys waiting to exit the Line at the current Station, then notifies the Journeys waiting in the Station to board this particular Line.
In summary, I use a lock on each Station to make sure only one Train can be in a Station at a time, and I use condition variables with .wait() and .notifyAll() to signal the Passengers to move through the Stations and Lines.