Utilizing the Transfer Utility

Rane

Okay, so I'm having difficulty either A understanding exactly how the transfer utility is supposed to work, or I'm just doing things wrong.  What I have is a ship that I'm rigging and due to the somewhat annoying inhibitors with the whole 'Object's geometry cannot be updated because the vertex and facet count must be the same" I find myself having to re-rig the entire thing from the ground up, for the third time.  What I'm attempting to do is use the transfer utility to copy the bone structure, locations and limitations to the new instance, since really only the UV mapping and some small geometry details are different.  

What I get however, is not so much a perfect copy, but one where all of the geometry stretches when it really shouldn't.  I'm wondering how to fix this.