So I spent some time playing over the last few days with the layout, and fixing my car. I've arrived at this layout here and I think I'm happier with this. The yard on a turn makes for a difficult situation coupling cars, but uses less straight track for longer trains as, I think it was, @OilValleyRy suggested in another design I had. I've got the wye back in there. There are also a few more sidings for other industries as a result. The intermodal yard is near the railyard/part of it. I don't like the S but that's the only way I could make it work in AnyRail. I'd like to make a second siding near the town if I can but I'm just going to get this out on the benchwork and see what happens.