Thanks for the observations. From what I presented I can see your concerns.
However, the cars and trucks are in this layout are horses and wagons. At your suggestion I will smooth out the curves in the roads a little.
The long straight track above the roundhouse is a trestle with the actual elevations in the corners and around the pipe, and although they are a little steep in places, they will be covered with trees. The upper right corner is a also a trestle above a canyon and falls.
The lower right area will be lifted off my old layout. You can see how I handled the "retaining wall problem."
Chip
Building the Rock Ridge Railroad with the slowest construction crew west of the Pecos.
When you ask for comments on "glaring" problems, then to me that means you want to hear about what sticks out, and shouts "Alert!". To me, what jumps out at me is the lack of scenery space, considering what you intend to fit in. I commend you on developing a plan that locates not only the buildings but also the roads and streams... not everybody goes to that level of envisioning, but I believe that it can really pay off. However, I think you have underestimated the "footprint" of these elements, like the width of the stream course (it needs to be wider than the shorelines), the need for shoulders on the roads and preferably curves of a certain minimum radius. For cars and trucks to navigate a road, it needs curves of at least, say, 40-foot radius (centerline); you might cheat this a little bit, but even a 4" radius (real dimensions) would feel a lot more natural than the hard right angle you've shown.
How might you achieve these goals? If it were me, I'd consider giving up a siding or two. But you could also just do some things such as let the stream go into a culvert and the road can wiggle over it; in the real world, this happens often, as the road follows the stream course and the old stream just gets buried. You might also elevate the roadway and have it cross the tracks by bridging above, rather than at grade.
That's what jumps out at me. I so often see great layouts compromised scenically because of a lack of sufficient space given over to the scenery elements - they end up with train-height retaining walls everywhere, or unrelenting cliff faces, or any of the other standard tricks to deal with the tight proximities. But these features are nowhere near as common in the real world, and so no matter how skillfully done, the scene just doesn't look real.
Well, I regained right-of-way in my basement. I know you guys have seen a million plans from me on this subject, but I think the time has come to actually build. Please let me know if you see anything I am missing.
A couple of notes:
The top yard track is a caboose track.
The 4% grade leads to the staging that simulates the lumber cutting operation.