Mesh Tool cannot work with the Hi-Res meshes, as it pulls the vertex references from an original Maxis mesh, which the Hi-Res meshes don't match. They must be done manually using the Unimesh tools in Milkshape to create the .simpe files. I use the Mesh Tool only for resizing Maxis meshes without adding any verts, but as soon as you actually modify the mesh in any way other than moving stuff, you can't use Mesh Tool anymore.
One other thing... there is a very specific reason why I never made any of my Bodyshapes into a default replacement set. Once you start making a different size from the base Maxis a default, you are fairly committed to making every single clothing mesh in the game into that size, for all the EPs and the base game... otherwise it just doesn't work, because anything that isn't updated won't be the right size. This includes all custom meshes too. The sheer volume of work involved is just mind-blowing. That's why I've stuck to custom sizes, and a limited selection of clothing for each shape, just to keep my sanity, and let others build on the work. The actual process of making a mesh into a default replacement is very easy, but the ramifications need to be considered carefully.
So... all the posts you have made that say "Hi-Res" you actually took the default Maxis mesh and then added verts to make it look better? And when we simply use the magnets and MeshTool its not quite the same result then.