When I was there in 1953 there was an O-Scale Santa Fe model railroad right where they lowered that Stuka. The Stuka, Spitfire, Boeing 727 and Engine #999 were not there in 1953. I do see they still have a model railroad.

A little googling revealed the O-Scale model railroad has been replaced by an HO model railroad. I didn't think HO was suitable for large museum operating displays.
More googling found Bill Davidson, MSI's Train Guy. Bill says, "HO trains just weren't designed to run 8 to 10 hours a day. It is a constant battle to keep them running all day long."
=> http://chicagotonight.wttw.com/2013/07/ ... -train-guy
Just as I thought.
P.S. on the O-Scale railroad.
The Chicago model was built at an unusual Q scale, which derived from the fact that O-scale trains were supposed to be 1/48 of life-size, but the tracks were just a bit wider, at 1/45th of life-size. Meticulous modelers like Cronkhite decided to build everything at 1/45th scale, which they called Q scale because a Q looks almost the same an O. The brochure says the Golden Gate model was 1/48th, so it may be true O scale.
Reference: http://streamlinermemories.info/?p=4463 --Thank you to Jerry (aka gnnpnut) for the reference.
Edit 1: Fixed broken link.
Note 1--See Sarge's correction on scale and gauge for Q gauge in a later post in this thread.