I like the connection between the upper and lower levels, that looks like an interchange between two railroads.
I use gargraves track and ross switches, and it looks like the plan itself will work for running trains. If you plan on modeling other than the CNW, your trains on the outer loop will be running counterclockwise, so that spur on the left isn't going to be easy to access, plus it faces against your yard. You may want to run it off the middle of the curve, oriented north south rather than east west, and put the switch at the other end so deliveries by local freights can be picked up by your yard engine and shoved back to the yard.
As for the upper level, it looks like you have an operating loading dock of some sort. In the real world, this would be on a spur, not alongside the main like a passenger staion. You could put it along the spur to the left.
Your backshop looks good, but one of your yard tracks comes right off the main, and puts the main through the curve of a switch. Experience has made my shy away from this, as some engines that can handle a normal curve will still derail going through the switch curve at speed.
All in all, though, I like the two levels, and it makes me think of a class 1 on the lower and a short line on the upper, with an interchange.
