The project is using an existing old tunnel under the river that was refurbished to handle the increased usage. They had to drill two new tunnels from Long Island City to connect with the portals at the river. Sunnyside yards have been dramatically transformed to accommodate the new ROW's. New tunnels and platforms were built deep below Grand Central to handle the trains.
Unfortunately by the time they get this project done there will be no reason to go into NYC anymore 
