There's nothing particularly difficult about it, beyond working out which bits you want to obscure which other bits. In this case, the hood would need to be at the top of the hierarchy, then the mask, then the head I would suggest.
Odd, I wouldn't think simply changing the mesh alpha would cause a crash. 5K polys is not particularly outrageous. My protocol droids are pushing 20K, so I doubt that is your problem. You mention you are using a single body model. What are the mesh splits like? What about shadow casters? I have had many crash issues with custom meshes caused by shadows. Are you casting shadows from the mesh, dummy shadow caster meshes, or the skeleton?