So, here's my latest version. Somehow I lost my SCARM file, so it'll take me a bit to recreate it from a backup.
Ok, thanks to auto backup each time I save that didn't take as long as I thought it would. Somehow the header got corrupted and the original file wouldn't load.
Anyway, I think I addressed all the concerns, though they might not be the most desirable solutions. I thought I mentioned the switch problem across the river and through the town some time ago, they're both the same situation, but maybe I never posted my comments. Be that as it may, mainline2 now runs through the straight section of the switches for the entire run. The yard now allows arrivals and departures in either direction with long lead tracks so there won't be any fouling of the mainline. To do all this, I had to add the 2nd bridge over the river and another cross over the entryway. I know that's not the most elegant solution, but the dual track bridge can be a lift out/up and the new cross can be a simple dropdown or another bridge.
I changed some elevations below the entryway so the out run is a bit higher than the others. That's why the Blue tracks are so much longer than the orange tracks. I updated all the grade and track height labels, so you can take a look at those by turning on those levels.
One question I have is what are the other bridges you already have and how long are they. The ones I used across the river might be too big or not big enough.