James,
Forgive me for butting in, but this will not fit in a 55" x 59" space.
I didn't understand how 3 layers at 1.5" were used to determine the height, so I did this version with the upper level and trolley loop 4.5" above the base. A quick search didn't find the height of the PE engine, so I'm not sure that's enough with tracks and upper level decking. Though the photo shows just the tracks, the tracks in the attached file are set to Bridges w/o supports so you can see the separation in the 3D view easier. Various sections have also been placed on different layers so they can be turned on/off. I didn't mess with setting tunnels or adding objects for decking. I'll be more than happy to help you with learning how to set grades, etc.
Anyway, the thing about clearance is it needs to be wherever one track overlays another, not just between levels.
As you can see along the left and top, the upper pink tracks overly the lower blue track over most of the grade and there are places where clearance is than 1.5".
The outer blue grade tracks along the top are too close to the lower level green tracks, trains will hit the tracks.
The inner brown grade tracks are also too close the the upper pink tracks and clearance over the green tracks is also less than 4.5".
The purple trolley loop is also too close the pink upper level tracks.
