The clues are given in three images located on: the train wall, the top of the south station hatch and the underside of the train:
The panel on the rear of the train tells you where the 3 crystals are and where one of the symbols is. The drawing on the hatch tells you where more symbols are. The gaps are filled by combining the symbols on either side. The arrow points to the tuning controls at the south station.
You will need to rotate this image and the one from the underside of the train until the tuning controls are in the correct relative position to the crystals shown on the image on the train wall.
You can now relate numbers to symbols to give the following:
Crystal 1: hexagon and hourglass, 8,2.
Crystal 2: square, 2,4.
Crystal 3: triangle, 1,9.
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