sorry for the strange name, I couldn't think of anything better.
Basically my idea is to avoid building 3D-Floors, but build a collection of sectors of the same outer shape (lets call this an area), and place things with the same tag number at their outer vertices. Those sectors would need to have such heights as to be 'above' each other.
Then, somewhere in the map there is an area with the same outer shape and size, and there one places things at the vertices to mark it as the 'receiving' area, and the sectors are moved to be there.
Sectors of the same size and shape which floors and ceilings touched would be vertically merged.
I think this would often be much easier than to build 3DFloors, and be more flexible and 'doomy'. One just needs to define where to stack, and could define the connecting holes, and vôila!
Explanatory image:
