There are a couple of areas where I don't think there's enough separation. In the top circled area, the brown grade varies from about 3.5" to 4.25" above the green bottom track, so even without sub-roadbed, the engine and cars are going to hit. In the bottom circled area, the separation between the purple tracks and brown tracks by the switch varies from about 4.5" to 5". Also, the grade ends inside the tunnel and depending on the opening, the tops of boxcars could hit the sides of the opening.
Here's some suggested changes. I rotated things 90° to get a larger workspace on my laptop. The dark blue tracks are at 6" and the single dark blue switch is at 5". You can see the grades and I ended the brown grade before the tunnel. Unfortunately, there is still only 4.5" of clearance beneath the turnout and I'm just not sure that's enough. You can changed the height of the dark blue tracks to 6.25" and that will change the grades to 3.7% and 2.7%. Just food for thought........
