some years back I was working on a crystal for swarovski. I had exactly the same problem you describe here. by that time there was no solution at all (script-wise) other than working with booleans (pure handcraft and calculating faces with pen and paper ). I think those kind of modeling jobs belong into the section of solidWorks, AutoCAD etc. I mean real construction & engineering software. Since maya is far from class A surfacing (in terms of precision and available tools), I found that the only working procedure was to stonecut the desired shape out of a polygon cube.
maybe someone else can propose some more usefull idea, but I´d try with booleans. (prepare for maya crashes tho )
everything starts and ends in the right place at the right time.