The majority of the train remains the same. In fact, the approach to Jerusalem is still mostly the same as well. Upon entering the vicinity of Jerusalem is where the old and new diverge; the old went through Baka ending up at what is now known as the "Old Train Station," a defunct train station now be turned into a museum. That train station is right near Emek Refaim, and between Derech Beit Lechem and Derech Chevron. The station is right near Gan Hapamon and the Inbal Hotel. The "new" train basically enters Jerusalem and ends its route there at the Malcha train station, right next to the Malcha mall and Teddy Stadium, in Malcha, Jerusalem. I'm not sure how overdue the train is, as CityPass, the light rail in Jerusalem, is the landmark overdue train in Israel! The new route is much straighter and then ends up at a new train station being across the street from the Central Bus Station in Jerusalem. It should be finished in 2015 or so.
The train will also stop at Ben-Gurion Airport (Terminal 3) and then Tel Aviv, though there's a chance they will extend it to Malcha, as well as Modiin.

You can see more here: http://en.wikipedia.org/wiki/High-sp...y_to_Jerusalem

I remember taking the train from Jer to TA with my daughter during a school holiday "for the experience". She is now a 35 yo mother of 2 - so that gives you an idea of how long ago. Seems ot me that the train slowed to about 10 km/hr for most of the curvy ride to Beit Shemesh. Maybe one day the capital of Israel will actually have an efficient train service. In the meantime, they say that the first passenger on the Jerusalem light rail will be the moshiach!

What type of hat/kippah will he be wearing? As a chayal, he'd be able to travel the train for free!