I live in NYC and ride the subway regularly, so I'm pretty much in the same boat (train) as you.

Riding the last car is a good idea, although at night I usually ride in the front car, both because only the front of the train opens at the station I usually go to, and because that's where the motorman is, should I have an encounter with some malcontents (of the ordinary hit-you-over-the-head-and-take-your-wallet criminal variety) - the back of the train is pretty desolate late at night. Otherwise I usually ride in the last car.

I'd definitely upgrade the flashlight - I carry a Pelican M6, although any of the Streamlight or Surefire line would work as well. If you're going to light up a subway tunnel, this is the way to do it. If you've never seen one of these lights before, you must.

My jacket has a back pocket (like a game pocket) and I keep a folded orange reflective vest in there.

Also, being a ham radio operator (call N2ZLQ) I carry around a Yaesu VX-7R. It's a ham transceiver, but with broadband RX coverage, and I have the transit frequencies programmed in, so if the train gets stuck someplace I can hear what's going over the radio. The PA announcements are almost worthless, although even the stuff that goes over the air isn't the most useful either - NYCT keeps their road crews woefully uninformed.