John, I don't see any "S" curves, but then my eyesight isn't what it once was. An "S" curve is where there are 2 curved tracks connected together that go in opposing directions. The solution is to add a straight track between them, usually a 10" or longer track. This eliminates the stress on the cars and couplers from getting pulled in opposite directions at the same time. It appears you'e done that.
I would like to take this opportunity to remind you that by adding the O54 curves, you are limiting the size of engines you will be able to run. That means you won't be able to run anything that requires curves larger that O54, like the MTH Premier 4-8-8-4 Big Boy steamer. Personally, I don't have a problem with it because anything I buy will run with O31 curves, but I felt I needed to point out the limitation you are imposing with the tighter curves.
I'd also like to take a moment to discuss grades. I noticed some of the elevations got changed to 3" and that just won't work, so I changed them back to 6.5". Then I fiddled with the subway grade at the top of it's run. You can see I moved the beginning of the grade (Blue track) which changes where it will appear (Orange track). It also increased the grade to 4.7%. Have you considered an auto-reversing trolley instead of a subway?
I wasn't sure about the "S" thanks for clearing that up. As far as large trains small curves, at present the largest I have are 4 - 18" passenger cars Lionel 19079 heavyweights and a Diesel set K-Line K28701H which are 17.5" long. They are huge compared to the rest of my collection and although they look fantastic, if they won't work or look out of place I might sell them and get a smaller replacement. Not sure on how that will pan out yet. I did get a good deal on them at the time a couple of years ago. I still haven't taken them out of the box to run or test.
The 3" elevation was me playing with scarm table depth and valley terrain. I think adding the "subway" threw things off so to speak. And yes you are correct, this is by no means a final layout, but scarm practice and getting an idea what is possible in the space I have been given. Again which came first Chicken (design wants) or the egg( actual room size and layout constraints)
I picture the subway will be it's own layer under the table and then at the end elevate up to end at Coney Island. So it will skirt the edge of the table as much as possible with stations along the way. Not sure how far below main table it will/should be yet. The subway will probably be last part of the build, if it gets put in the end design at all.
Again Thanks Dave.