I saw your post last night
I saw your post last night but I lost my reply (I log in and then the site automatically logs me off not a half hour later??? yuck!!!)
But Anyhow...
I had a similar thought in mind, though I had a bit more elaboration you might like. In your image, you have old logging on the upper deck on both sides. In my version, I basically let the aisles do the time separation.
Your place names gave me a direction to start researching, and there I found some rich information.
You might start with the Wikipedia page for the Pacific Great Eastern. This railroad was supposed to run from North Vancouver to Prince George, but for 30 years it only went from Squamish to Clinton - a perfect "nowhere to nowhere" railroad!!
Now this railroad was eventually finished as the BCR, before being rolled into CN. And CN provides you with a second route of greater importance, the Canadian transcontinental line from South Vancouver up over the mountain to Calgary.
I then drew a layout schematic, taking into account this historic information and your physical parameters.
In this diagram, the outer loop represents the upper deck while the lower loop represents the lower deck. The middle area represents your grade section, in which case you have to rise up 24" and at a 2% grade that means you need 100' of total run to get up there - a total of four runs, or twice around the middle island for your mainline. The dashed area represents the end of the room where you might have to contend with a door - I have no idea where your door is, but it probably wouldn't matter one way or another.
Notice how a train from Squamish cannot run straight into South Vancouver, and further, a train in Calgary can't run straight into Clinton!
You'd run in the left aisle as if it's modern day. The route starts in South Vancouver, goes up the grade and then terminates in Calgary, with a line leading off to your "Canada East" staging yard, perhaps in the dashed area. The Right side would then represent the PGE, or BCR, from Squamish to Clinton.
How you thread this through the middle would be up to you, but I'd do it in such a way that you'd have two major vignettes in the central island, one on each side, representing a town halfway between the lower deck cities and the upper deck cities. There would be holes deep enough in the central island such that you'd be able to access switches and see the trains in the proper places without having to ever going to the opposite side. If you were really cleaver, you;d put in passing sidings in such a manner so that if you were running both sides simultaneously, you could minimize the amount of time an out of era train appears on either side of the layout.
Now you see the dashed area...and here things get interesting. Let us suppose you connected the layout on both upper and lower levels, with 4" wide bridges at the doorway. This now allows you to insert the Prince George yard, and run from North Vancouver up to Squamish. From there, you'd go up grade to Clinton and then Prince George, before heading south to Calgary and then back down grade, terminating in South Vancouver.
The line out of South Vancouver may even be 4" lower than the Squamish line, to accommodate that 4' of concrete you have to contend with, and cross under the Squamish [hidden] line. After about 16', though, the two lines would be at level grade with each other. But that's more complexity to deal with later...