Just finished laying down the track on the base level. I ended up gluing two layers of cardboard on top of the MDF base, since I didn't think the MDF would make a good working base for the track and structures. I used wood glue and let everything dry for 24 hours. The different layers (4 now) should prevent warping of the flat surface. Since neither the MDF nor the cardboard is suitable for traditional track spikes, I did a test with a small piece of cardboard and some extra Atlas 80 track, and just using PVA glue I found I could fix it to the base really well. In the future I can also pull up the track by pulling apart the cardboard. The two cardboard layers give an extra bonus: I can carve through them to add depressed areas on the layout as well.
Each section of track was glued to the cardboard with PVA, weighted down and allowed to dry for at least 12 hours. Our cat helped again, as pictured. I did learn an important lesson - even though it seems easier, do not fix the track in sections, because you might find out that the ends of those sections are slightly out of place. Although I transferred the key track end locations from the full-sized printout to the baseboard, the track and the glue conspired to introduce some kinks into the line. After each section was in place I ran the loco around a few times and it seemed fine, but it's the transitions between sections where the tangents are slightly off-center. It's nothing that should be a serious, track-ripping problem, but I will have to be more careful when I lay the upper level. I did figure out a good way to use the natural channels of the corrugated cardboard base to hold the feeder lines to the track. I probably added too many for such a small route, but I wanted to be sure that my locos have enough power no matter where on the layout they are.
Speaking of which, I went ahead and ordered Branchline's N Stoney Brook Bridge kit as well as a more modest N 75-153 Deck Girder Bridge from Micro Engineering. I wanted the bridge kit to have something "modelly" to work on, as well as to have a good-looking structure for the overpass, since it will be near the center of the action and an important detail on the layout. The girder bridge will be on the edge, near to where the line continues on to imaginary and distant locales, so a more simple structure seemed appropriate. Everything from Micro Engineering always looks very well-made as well; I thought about getting a classic Atlas or Model Power truss bridge, but the pictures just looked too toy-like for my tastes. Both of these bridges are well within the realm of possibility for a Japanese colonial-themed route.
After ordering the bridges, and with the main level track fixed, I realized that since the branchline bridge has an arched support structure, the track below would have to pass under the middle of the bridge in order to maintain its overhead clearance. Unfortunately the original plan had the lower track passing near one side. So I opened up XTrackCad and moved some things around. I think the result is even better than before, and I didn't have to modify any track that is already in place. The wooden kit bridge will have even more space, and the opening between the "bowl" and the main yard/station area is now wide enough to justify a dirt road or something leading in to it. I am thinking that a mine would be a good industry to stick in that narrow space, similar to the small mines on the Pingxi line in northern Taiwan.