Some rough ideas. These are to be used with the Armor as DR variant rules (though probably with some modifications). All of these are subject to change, but text in red means that it's under more serious scrutiny.

• In this system, a critical threat is considered a critical hit and automatically deals maximum damage, but is not multiplied. Instead, it subjects the target of the critical hit to a Fortitude save equal to 10 + 1/2 the attacker's BAB + the attacker's Str or Dex bonus, whichever is higher, + 2 per step of the weapon's critical multiplier beyond x2 (+2 for x3, +4 for x4). For example, a critical hit from a Minotaur would deal 24 points of damage and would have a Critical Save DC of 19. A critical hit from a 4th-level rogue with a +4 Dex bonus wielding a rapier would have a Critical Save DC of 15.
• Armor functions as Damage Reduction against spells and elements as well as regular damage, or they add to reflex saves. Not quite sure yet. Spells become an issue at high level, and this is the way I'd like to test to deal with it. Armor not protecting against elemental damage has always seemed silly to me. Even padded armor is the equivalent of hot pads, and firemen don't wear those heavy suits to look pretty. All forms of armor have some form of padding underneath, so they should provide protection against heat, insulation from cold, and even insulate against electric attacks (though I'll probably use rule from psionics that wearing armor gives the caster a +2 to attack or imparts a -2 penalty to Ref saves when using electric spells/effects.)
• Wound Points are equal to 2x Constitution Score, though this can be modified by feats and other things. St. John the Destroyer has a Constitution score of 12, so he has 24 Wound Points.
• Any damage received is applied to Wound Points.
• Wounds are tracked individually, not cumulatively. If St. John takes 4 damage from one hit, followed by 6 damage from a second hit, he tracks them as a 4-damage hit and a 6-damage hit, not 10 damage total.
• A Minor Wound is anything less than 1/3 your total Wound Points. Minor Wounds do not reduce your Wound Point total while in combat. St. John takes a hit that deals 5 damage, after his Damage Reduction. Since 5 damage is less than his Serious Wound Threshold of 8, the hit is considered a Minor Wound. St. John makes a note on his character sheet but he still has 24 Wound Points.
• A Serious Wound is anything between 1/3 and 2/3 your total Wound Points. Any time you take a Serious Wound, you are staggered for one round. Additionally, you take a cumulative -1 penalty to all rolls and checks for each Serious Wound you have sustained. St. John takes a hit that deals 9 damage, after his DR. Since 9 damage is more than his Serious Wound Threshold of 8 and less than his Deadly Wound Threshold of 16, the hit is considered a Serious Wound. St. John makes a note on his character sheet, is staggered for the next round, takes a -1 to all rolls and checks going forward, and has only 15 Wound Points remaining.
• A Deadly Wound is anything more than 2/3 your total Wound Points. Any time you take a Deadly Wound, you are staggered for 1 round and you take a -5 penalty to all rolls and checks. Additionally, if you take a Deadly Wound that would not drop you to below 0 Wound Points, you must make a Fortitude save with a DC equal to the damage dealt. Success means you suffer the effects of the Deadly Wound as normal, while failure means you drop to -1 WP, are disabled, and begin bleeding out. St. John takes a hit that deals 21 damage, after his DR. Since 21 damage is more than his Deadly Wound Threshold of 16, the hit is considered a Deadly Wound. St. John makes a note on his character sheet. If he had at least 19 Wound Points remaining, he would make a Fortitude save with a DC of 19 that could allow him to remain standing at 0 Wound Points, staggered for the next round and taking a -5 to all rolls and checks going forward. However, since he only has 14 WP remaining, he drops to -5 WP, is disabled, and begins bleeding out. 
• After combat is resolved, Minor Wounds come into play. If you have at least one Minor Wound, you take a -1 penalty on all rolls and checks, as if you had sustained an additional Serious Wound. If you have more Minor Wounds than your Serious Wound damage threshold, the penalty is -2. If you have more Minor Wounds than double your Serious Wound threshold, the penalty is -3, etc. If St. John had sustained more than 8 Minor Wounds in addition to his Serious Wound, he would have a -2 penalty to all rolls and checks, as if he had sustained two Serious Wounds. If he had sustained 17 Minor Wounds in addition to his Serious Wound, he would have a -4 penalty to all rolls and checks as if he had sustained four Serious Wounds. I really need a better way to write that, the current model is definitely too wordy.
• All wounds that a character receives heal naturally at a rate of 1 point of damage for eight hours of rest, or 2 points of damage for a full 24 hours of rest. Receiving long-term care from someone with the Heal skill increases the rate of natural healing by 1 (2 points of damage for eight hours of rest, 3 for a full 24 hours). If St. John had sustained four Minor Wounds of 2, 3, 5, and 7 damage, after one night of rest those would become Minor Wounds of 1, 2, 4, and 6 damage. He will need at least two nights of rest to recover from the lightest wound, and a full eight nights of rest to recover fully. Alternately, he could rest for four days straight and be fully recovered. 
• Magical healing works as normal, except that each cure spell can only target a single Wound. The healing from a heal spell may be divided up to heal multiple Wounds. Should fast healing/regeneration heal all Wounds at the same rate? If a troll takes a Minor Wound of 12, a Minor Wound of 14, and a Serious Wound of 25, does he reduce those to 7, 9, and 20 all the next round? Or should the fast healing/regeneration be split up among the existing wounds? Will have to test the math and see.
• When a Serious or Deadly wound has been reduced, naturally or magically, to below the threshold of a Serious or Deadly Wound, respectively, then the wound is downgraded to the next lowest type of wound. St. John has a Serious Wound of 9 and a Deadly Wound of 21, and is receiving long-term care while undergoing complete bed rest. After one day, the 21-damage wound would become a 18-damage wound, and would still be considered Deadly, imparting its -5 penalty to all rolls and checks. The 9-damage wound, however, would become a 6-damage wound, and would be considered a Minor Wound rather than a Serious Wound for purposes of determining wound penalties.