Okay, so this doesn't "fix" any problems, and please understand this is merely a suggestion. I in no way intend to hijack your design, and do not expect you to use the suggestions. Simply food for thought.
Excuse my excellent MS Paint work, but it was the easiest way to show my ideas.
From the top
- I added a track next to the blue. This can be either a staging area for your coal cars, or a locomotive run around. For the same reason you added the runaround at the coal mine, you'll need one at the bottom of the hill. The idea is to never interrupt the main line when moving cars around.
- I shortened the lumber yard rails. Since there really isn't a way to get more than maybe two cars out at a time, there is no need to be able to store 8 on each line. In fact, the lines are probably still longer than needed. Save your money here and don't lay the extra track when it can't be used.
- I connected the lowest yard track to the main line. This is your staging for the freight yard. A train traveling on the main can drop of cars here and go about it's way. Then the switcher can do it's work in the yard without interrupting the main line. Again, all operations should not interrupt the mainline.
- Going along with the aforementioned mainline interruptions, the passenger station is on the mainline. Is the outside main only for passenger use? If so, this may not cause any problem. If not, maybe a siding there for the station would help.
- I see that most of the track is sectional in the design. My suggestion would be to use flex track as much as possible. It will minimize the number of joints, thus minimizing the possible locations of problems. This completely up to you though, as many people do prefer the sectional over flex.
Again, only my two cents. Take or leave it - I can use the money if you don't want it!