Alright, so the city journal thus far has not focused that much on rail infrastructure. That's changing.
Portdale was always a major city for trains; New Haven had a major foothold in it. The majority of Commuter Lines were originally NH, being purchased by PTA following Penn Central's formation. The main Passenger Yard of Portdale is the already-covered Hayward facility, and there's smaller yards near the end of every line. Union Yard, located near Union Station, holds trainsets for the Rush Hour, preventing a deadhead. The main Citylink/Amtrak Yard is the Caller Facility, located in a rapidly-gentrifying industrial part of town. Switching for it is currently the duty of a leased BN Geep. Union Yard is usually the domain of a GP40, purchased from Springwood Lines after it was absorbed. Union Station serves trains from both directions. Northward, you have the Bay Trunk lines, radiating in a U-shape away, the Davenport line, a black-sheep from an Interurban bought up by the City, the Valley DC Lines, and the Cliffside Line, with sporadic service from the Space Ctr Shuttle.
The first stop for most Northbound trains is Newtown; having 6 tracks, 2 reserved for the (2) Subway, and 2 in each direction for the PTA. Most PTA trains head to BFI, covered in previous posts and now a major junction; 2 subway lines, Skytrain to the Terminals, several train lines, the Monorail, a LRT and Bus Service; it's one of the busiest PTA stations by volume. The monorail was a pet project of late mayor Jacobs; the Subway was overburdened and the suburbs had exploded. He ordered the construction of 2 lines- 1 to the city and 1 remaining outside. Both are fairly popular.