Working with three or four different programs here, none of which are completely the answer in themselves (sorta like my four stories?). This is why Adobe has what they call "suites" — to make sure all elements can be done in their suitable programs, then combined. Too bad the whole combo still doesn’t fit my needs exactly, and the CAD programs aren’t compatible.
I’m still thinking along the lines of the different planes of vision, similar to that Graphite clip I mentioned. Picture four "floors" (stories?) with various objects laying about, a sphere, a cube, a pyramid, etc., and connections between the levels of floors that are threads of communication or progression–stairways. Each object might be colored differently, zoomed up to the forefront with a click, and opened, like a Christmas present, to reveal a mini-movie, text, images, music, whatever.
I’m not building just a story here; I’m building a house.