I had some of the problems you are having when I scratch built the section house in Sn3 about twenty five years ago. I used the photos I could find and Mike Blazek's plans. The problem I had was dealing with the slope the section house is built on. The add ons were affected by the grade. I built the structure to fit the contours as best I could. This is a definite compromise, but some of the slope has to show to make it look right.
The second issue was that the Highway 17 trestle is a lot closer to the section house than it appears in photos. ROW diagrams put much of this into perspective.
Thirdly the depot and the track near it have changed over the years. In perspective the depot is a lot closer to the section house than you would think. Likewise the depot width is a lot narrower than most of us imagine it to be.
Good modeling to you.