I'll take a stab at this. We seem to be struggling with the yard area. Lets just think outside of the box for a bit. How about losing the tunnel on the NW side and sliding the town and mining branch switch up along the curve. Use a Peco or Walthers curved turnout. The siding and town would sort of flow NW to SE and rework the spurs a bit.
Sliding the branch spur up into the curve gives you space to slide the yard and runaround tracks north and allows for more room in the SW.
You should still have room to have a small river in the NW corner.
That's a good idea, but it's a pretty major change. I've already build the frames for my benchwork and spaced the frame out based roughly on this plan. I like the tunnel in the NW corner because it breaks the scene up and gives the illusion that the train has traveled farther than it really has. What the plan doesn't show is that the mainline begins to climb 2.5% through the tunnel until it gets to the first bridge and then begins back downhill past the second bridge. I thought that having the mainline higher than the spurs would separate the scene so that there is not too much going on all at once. This is supposed to be a mountain railroad with lots of scenery, so I had to leave quite a bit of open space. The local train show is tomorrow, so I'm going to start buying up some track. I've also made another revision to include more walthers #5's instead of atlas #4's. The Atlas turnouts are cheaper, but are nowhere to be found right now! Even with the changes, I'm still short 1 Atlas 561 L #4.