I think I'm going to run with this for the next few weeks:
1- Toughness Bonus no longer reduces Damage.
2- Toughness Bonus is added to Wounds total.
3- Toughness Bonus represents a Critical Injury "buffer": A) when a PC receives damage resulting in a Critical Injury he/she may ignore (shrug off) the severe effects (the descriptive text) of Critical Injury results that are equal to or less than their Toughness Bonus (IE: an Acolyte with a TB3 may ignore Critical Injuries up to -3); B) each 3-point bracket of Toughness Bonus allows a PC to ignore the severe effects of one (1) Critical Injury (IE: PCs with TB1-3 ignore only the first Critical Injury sustained, PCs with TB4-6 ignore the first two Critical Injuries sustained, etc. [up to the limits outlined above]); C) regardless of TB, each time a PC ignores a Critical Injury result he/she must take a Challenging (+/-0) Toughness Test, with failure resulting in the PC suffering a level of Fatigue equal to the Critical Injury, +1 level of Fatigue per DoF, -1 level of Fatigue per DoS (to a minimum of zero  levels of Fatigue) (IE: a PC with Toughness 37 (TB3) ignores the severe effects of one Critical Injury result of -2, rolls 53% for his/her Challenging Toughness Test, and so suffers 2 levels of Fatigue [the Critical Injury result] +1 level of Fatigue for one DoF, for a total of 3 levels of Fatigue). This means PCs may shrug off the severe effects of one or more Critical Injuries, but may still be rendered unconscious due to Fatigue. D) Once a PC has shrugged off the severe effects of his/her maximum "buffer" number of Critical Injuries any further Critical Injury results are resolved as normal. E) Critically Injured PCs, even if suffering only from Fatigue, are still considered to be Critically Injured for the purposes of healing. A special note here: PCs with the Autosanguine and/or Hardy Talents are considered Lightly Wounded unless they have suffered a Critical Injury (not including Critical Injury Fatigue).
View Fatigue as if it were trauma shock.
In effect, PCs are considered to be at zero (0) Wounds, but lessen the effects of one or more Critical Injuries to Fatigue (or nil) results until they have reached the threshold of their individual endurance, at which point they are literally being stalked by Death.
Unnatural Toughness- Each Unnatural Toughness multiplier reduces Damage by its base value (IE: Toughness 44 with Unnatural Toughness x2 [total TB8] reduces Damage by 4 points), adds +1 to the maximum number of Critical Injuries that can be ignored (shrugged off), and provides a +10% bonus to the Challenging Toughness Test to avoid accumulating Fatigue (IE: Toughness 44 [TB4] with Unnatural Toughness x2 [total TB8; Ork Boy, pg. 98, Creatures Anathema] reduces Damage received by 4 points, can ignore 3 Critical Injuries, receives a +20% bonus to Challenging Toughness Tests to avoid accumulating Fatigue, doubling the number of DoS (standard DoS rules for Unnatural Characteristics). An Ork Boy wears Flak Armour (Body AP2, +2 [see below], total AP4), would have 20 Wounds, and the Hardy and True Grit Talents.
True Grit (Talent)- There are no changes required; the Talent works exactly as described on pg. 122 of the Dark Heresy Core Rules. In effect, this means PCs with this Talent are even more hardy and resilient. So, PCs (and NPCs) with the Die Hard and True Grit Talents are foes of considerable resilience.
Special: Daemonic Trait- Unless the weapon being used against them is a Blessed/Sanctified/otherwise Holy Weapon/Relic, creatures with the Daemonic Trait reduce Damage by their FULL Daemonic TB score. Weapons with the Qualities listed above will reduce a Daemonic TB by its base value, exactly as with Unnatural Toughness (see above).
4- All base AP values (aside from those of vehicles) are increased by +2. To be specific, this includes Primitive and non-Primitive armour, the Natural Armour and Improved Natural Armour Traits, Cover, and any AP provided by Psychic powers/abilities, and does not include the Machine Trait or the Flesh is Weak Talent.
5- There are no changes/alterations needed regarding weapon Damage or Pen values (at this time).
Some thoughts here regarding special ammo: Man-Stopper rounds behave exactly as their name would imply, and are quite good (within the game mechanics) of doing as intended. Dum-Dums, on the other hand, are disappointing and (within the game mechanics) useless. I've hit upon the following solution: Dum-Dum rounds will do +2 Damage to unprotected locations (such as a bare head…or a rabbit) and to "monstrous" creatures possessing the Natural Armour or Improved Natural Armour Traits, and reduce the effectiveness of 3- A) (see above) by -2 (IE: a PC with Toughness 37 [TB3] that suffers a Critical Injury caused by a Dum-Dum round can now only ignore up to -1 severe effects (descriptive text). So, Dum-Dums would be a viable ammo choice when shooting at Orks, especially since the majority of their lot tend to wear quite a bit less armour. Also a good choice when targeting Genestealers, but not so much when assaulted by professional mercs kitted in full carapace. Man-Stoppers for one task, Dum-Dums for another.
Now, consider the Genestealer (pg. 90, Creatures Anathema). Still a horribly dangerous threat; an extremely high Movement coupled with the Hard Target Talent, it may Dodge twice per Round at 70% (doubling its DoS), attacks up to three times per Turn (likely at a much higher Initiative), gets +2 AP (AP6 all locations), and increases its Wounds total to 22 (from 16). However, it does NOT benefit from the Critical Injury "buffer" House Rules. Why? Sure, it's a Genestealer, but to the Tyranids (and thus GMs…at least this one) it's just a mook. Ork Boyz might shrug off a few minor Critical Injuries with little or no Fatigue, but keel over dead with the first severe effect (descriptive text) Critical Injury. However, a Lictor might go the full distance…
Ultimately, it's GM fiat.
Note: This is primarily intended for use with the Dark Heresy Core Rules. Obviously, I suggest all creatures with the Daemonic Trait and NPCs with the Touched by Fate Talent use the above House Rules (1-4). Likewise, they should be ignored (insofar as bullet point 3, the Critical Injury "buffer") when considering mooks, goons, scrubs, etc. They may also be useful in Rogue Trader, possibly Deathwatch, but I'm certain they will fail if used with Black Crusade, especially when you consider the Unnatural Characteristics and Zealous Hatred mechanics as presented in that Core Rules set.