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Hmmm, well I think you would go ahead and make your new package, import the cloned object in Milkshape, then import the .obj file. Move the object and resize it if you have to. Then go to the group tab and rename the .obj group to match the original Sim mesh. Delete the original Sims mesh and export the file as a GMDC file. I'm not sure you have to do that last part, but if the mesh groups do not match the groups listed in the shape file, the object won't show up in the game.
I'm sorry if this is confusing D: