The "stomach_IO_geom" and "chest_IO_geom" are for chest and stomach expansion and contraction and are used in the "Animation_Controls/TORSO" Poses. You don't have to use them, you can use muscle movement for that if you like. If you do decide to use them, weight them last for the torso. First, do your weighting using the "stomach_geom", "mid_section_geom" and "chest_geom", get everything to bend the way you want, and then expand the stomach and chest using those torso poses to weight between those and the "IO" bones.
If you put together a FAQ, it would probably help a lot of people...you've been very thorough in everything else you've done, Rusty. Anyone that wants to make a tutorial, guide, chart, list or whatever is more than welcome as long as they make sure the information is accurate at the time it's made. I'm going to be doing some tutorials over the next couple of months as I put together a personal project, hopefully those will help people as well.