Couple of questions:
- What 3D printer are you using?
- How accurate do you need the shell out to be?
I use Makerbot’s Makerware for my prints and the slicing software will automatically create hollow fills to a given specification.
You could try duplicating your model. Go to deformation and select a negative value from the Inflate slider. Where the mesh gets messy use the selection lasso to hide broken areas. Once hidden go to Geometry > Modify Topology > Delete Hidden > Close Holes. Add a connection to the outside surface and then it is a matter of using the DynaMesh functions to boolean subtract the parts together. All a lot of work, you may be able to achieve what is require from a freely available slicing engine (depending on 3D printer).