Yes, the Lilly Belle, some rolling stock, and the yellow caboose are all there on display. I've been meaning to write something up about my visit to the museum on Labor Day with my girlfriend. That room where they are displayed in was our favorite of the whole museum, even though there was (in my opinion) one *very* glaring weakness in it. I'll talk about that in another post as it directly applies to the topic of Disney railroads.
Note that photos are not allowed in that section of the museum where the Lilly Bell is on display. Photography is only allowed in the entrance lobby and the observation deck/balcony at the back of the building. Flash photography is not allowed in the entrance lobby.
Also note that the museum has the nicest bathrooms in San Francisco. They're downstairs just below the gift shop. Don't miss them!
Take your time getting to the museum on the grounds of The Presidio. It was a real pain in the neck to find! Getting to it from our home in San Jose was next to impossible.