Create a new train station using vanilla template. Then bulldoze existing train station track after clicking 'Make All Segments Editable' toolbar button (provided by my More Network Stuff mod. Place elevated track after clicking its button in 'Trains' section of the roads panel (More Network Stuff provides that button). Make sure you've placed only one station track segment. It will be shorter than you need. Now you need to resize it. Click 'Make All Segments Editable' again. Remember id of 'Station Track Eleva' segment (from console output). Run this script[gist.githubusercontent.com] (by @boformer) from ModTools console to change segment's length and elevation (replace values you need including remembered segmentId). Place pedestrian paths to make the track accessible. My proof-of-concept implementation of an elevated train station is available here. It's just a regular train station with an elevated track. Working though ;)