OK, here’s the plan I came up with.
There is a one foot grid on the plan. Elevations are marked in blue. The staging yard is at 0", the town is at 4.5", and the city is at 9". It’s actually fairly simple, though the small space and hidden staging under the town make it look more complex than it is.
This plan is based around putting a 1/2" plywood shelf over the center section (top at 4.5", 4" clearance underneath) to provide a location for hidden staging. Holes in the fascia would allow access. The yard is double ended, can hold 4 six-foot trains, and uses a pair of pinwheel yard ladders. The tunnels are designed so that a 6 foot train would always be visible from one end of the tunnel or the other. There is always 4" or more clearance when one track passes over another, so there should be plenty of room for supports and roadbed. Some cutting of the incline sets will be necessary, though. Large flat areas besides the town could be supported on plywood as well (namely the city scene and the coal mine), and this would save on materials.
This layout plan has a ruling grade of 2% heading to the right out of staging (4% with helpers for a short stretch), and 3% heading to the left. This is a great excuse to run double-headers and pushers on short trains, and the tunnels will make the train look much longer than it really is. And if there are serous problems with traction; use Bullfrog Snot - it works great.
Now a virtual tour of the layout.
Heading to the rig