Just out of curiosity, what type of 3d printing method will be involved in the creation of this piece once it's finished? Will you be printing the model using FDM, SLA, SLS? The reason I'm asking is that some methods may not require you to boolean the separate pieces. Shapeways uses SLS technology and two intersecting bodies are be treated as a single manifold object as long as they are exported as a single unit or instance. The empty space inside the intersections would be considered solid, as long as there are no gaps between the individual meshes or shells. They must overlap. They will be merged (unioned) together into one single piece by the software on the other end before it goes to print anyway.

You might also try Mesh Mixer ( a free Autodesk product), which has the functionality to handle booleans like this. Perhaps it will be easier just to import the mesh there, and let it handle the rest.

______________________________________

My Store
My Free Models
My Video Tutorials
My CG Animations
Instagram: @luxxeon3d
Facebook: https://www.facebook.com/luxxeon