Alright, well whacking elves repeatedly has given me at least some insight.
It seems bleeding values can be between 0 and 3x the [VASCULAR], unless the layer contains arteries. If an artery is severed the bleeding amount increases by ~ 10. If a body part is completely severed the bleeding amount will be 3x [VASCULAR] if no arteries are present. If an artery is present it will be blood_count/100
Pain is much easier, it is 3x the amount of pain receptors. Note that this is only the case for cut layers and broken bones. Bruises add 0 pain. A warhammer blow that bruises the skin, fat, and muscle and then breaks the bone will only contribute 150 pain, where as a battle axe that cuts all the way to the bone will contribute 195 (15 + 15 + 15 + 150).
Contact area and surface percentage don't seem to have any influence on pain or bleeding. I also can't seem to find any reliable way to give a percentage for motor nerve, tendon, or artery damage (note I only did 20 attacks for each weapon for each body part, so ~500 attacks total, not very good statistics).
Strain is strange in that for all the edged damage the strain values were 50000 and for all the bruised damage the strain was 0. The only times it wasn't one of these two numbers is when a blunt attack broke bone.
Unfortunately I am still struggling with determining penetration percentage. I have tried using the equations from Urist Da Vinci but I am missing something. If you take, for example, my runs of attacking the right upper arm with a battle axe with a velocity modifier of 0 (which I assume the game translates to 1), in all 20 attacks the attack penetrated through 100% of the skin, 100% of the fat, and between 71 and 83% of the muscle. But none of the equations give me that outcome. I calculate the momentum of the attack, and the shear cost of each layer, but I'm not sure how to put those together.
Also, another level of complication, in several of my attacks with higher velocity weapons bones were broken and sent through other body parts. I think for now I will simply imagine more fundamental attacks and wounds, maybe the compound wounds can be added later.