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