Honestly, a part of me doesn't really want these body part raws/calculations even more muddled than they already are.
However, that said, a connection/relative location chart would probably be nice.
With THAT said, I don't think I want a direct percentage chance that damaging the liver would also damage the heart. I would rather that were guaged by a general "impact size" function, especially since we already have a "size" variable for weapons, as well as a "percentage of the weapon that hits", which should give us the basic area that a weapon will impact upon with a little maths. (Also, why would an eyelid stop 10% of ALL attacks? Wouldn't a spear piercing through the eye with a good, direct hit, be capable of going through it like wet tissue paper, especially compared to a limp-wristed punch?)
To diagram the problem, the current body of a creature in this game looks like this: Imagine zooming in on an amoeba or other single-celled blob creature under a microscope until it's nice and big. That's the upper torso. Another big blob is touching it, that's the lower torso. Three smaller blobs are also touching the upper torso, which are the head and both upper arms. No, don't imagine that they are in their proper arrangements, because they're not. They just sort of free-float around, so long as they are still touching the parts they are told to touch. All the other limbs do that to their respective parts (upper legs attached to the lower torso, lower leg stuck to the upper leg, foot stuck to lower leg...).
Now, we need tissues. Each of the amoebas, if you look, is made up of a core of "bone" layer, wrapped in a "muscle" layer, wrapped in a "fat" layer, wrapped in a "skin" layer, wrapped in a "hair" layer. (Yes, hair covers all parts of the body evenly unless you specifically specify it not to.)
Now, we need organs. These are more small blobs we stuff inside the body section amoebas, which then free-float somewhere around the bones and muscles layers. Kind of like worms wriggling in there. Oh, and remember that they all have arbitrarily defined relative sizes to one another. They have to stay inside their little amoeba containers, but free-float otherwise, except for the "mouth" or "eyes". The mouth, for example, is a roving blob on the surface, which you then open a bag of teeth up, and randomly dump the contents out on top of, like dumping sprinkles onto glue-smeared construction paper.
The problem, then, is that we need to have specific placement within a creature's body for this to make sense.
Honestly, the first thing I can think of (to be as accurate as possible) is to simply make a cartesian coordinate system, so that you have a grid inside the body location, and can assign body parts to specific relative locations in the body part. (This would have to be percentage-based, or otherwise a fraction, as this is, after all, relative location, so that having a [50, 50, 50] coordinate would be in the dead center of a body location.) Doing that, we could pin specific organs to specific locations (although I fear for sanity checking this... what happens when a mislabeling in the raws or just careless programming makes a heart that overlaps the space with the lungs, or a liver that sticks out of the body because it was put too far to the right?), which would also mean we would not have to specifically stitch every single organ to every other tissue in the area. We can also just stitch the head (or at least, the neck) to, say, [50, 50, 100] of the upper torso, and have it in a relative location to the rest of the body.
Doing that, if we simply make the attack have an attack area be something like a circle upon this little stitched-together rag-doll, which continues pushing force through the rag-doll (as a cylinder, I suppose, although something more hemispherical might be more accurate) until enough tissue resists the blow that the damage stops.