Some of the walls for this setup are 2 dimensional. I had to account for the difference. Any wall running the full length of the dungeon can be disregarded for the purposes of keeping the dungeon proportional. For example the exterior walls are automatically disregarded. Any partial walls inside the structure have to be accounted for in places they dont exist. So, I put in a spacer in the same location where these situations occur.
This means the dungeon is slightly larger than the map but over the scale of this dungeon it may be 1″ wider and/or larger but all the rooms and hallways still line up properly and the party can follow a module map.