The New Haven Line FL9s had to be from the Danbury Branch - the shuttle does a few runs a day in which it offers a change at Stamford rather than South Norwalk. The Waterbury shuttle, however, never runs west of Bridgeport as far as I know.
I've been away, so I haven't ridden the Harlem line recently. I'm glad they changed the name, although Brewster North did follow the old Central naming tradition for engine change stations - i.e. North White Plains, or Harmon North (now Croton-Harmon). When they extended electrification north along the Harlem line, they closed the old station on the site of Brewster North, which was known as Southeast (the township in which both the village of Brewster and the station formerly known as Brewster North are located). It's good to know the MNRR planners remember that sort of thing.