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I took a quick look at your file and see where you got confused regarding the overlapping stories. You specified space heights of 12 ft for the first story and 16 ft for the second story, while the stories themselves have heights of 8 ft. In FloorSpaceJS, the idea is that the stories stack on top of each other, and you only need to provide space heights if you want to override the story height to model, say, 2-story spaces. So I recommend that you expand the Stories pane, update the heights to to be 12 & 16 ft respectively, and delete all the space height inputs. That should fix the overlapping issue.

That said, I agree that something appears wrong with the doors on the 2nd story. I filed a bug report here: https://github.com/NREL/OpenStudio/issues/3267