Well it compiles; just synthtissue and TongueLoss now.

code/modules/mob/living/brain/brain_item.dm

@@ -7,7 +7,7 @@
 	layer = ABOVE_MOB_LAYER
 	zone = BODY_ZONE_HEAD
 	slot = ORGAN_SLOT_BRAIN
-	organ_flags |= ORGAN_VITAL
+	organ_flags = ORGAN_VITAL
 	attack_verb = list("attacked", "slapped", "whacked")
 	///The brain's organ variables are significantly more different than the other organs, with half the decay rate for balance reasons, and twice the maxHealth
 	decay_factor = STANDARD_ORGAN_DECAY	/ 2		//30 minutes of decaying to result in a fully damaged brain, since a fast decay rate would be unfun gameplay-wise
@@ -16,7 +16,7 @@
 	low_threshold = 45
 	high_threshold = 120
 	var/mob/living/brain/brainmob = null
-	var/organ_flags & ORGAN_FAILING = FALSE //whether the brain organ is damaged.
+	var/brain_death = FALSE //if the brainmob was intentionally killed by attacking the brain after removal, or by severe braindamage
 	var/decoy_override = FALSE	//I apologize to the security players, and myself, who abused this, but this is going to go.
 	//two variables necessary for calculating whether we get a brain trauma or not
 	var/damage_delta = 0
@@ -103,16 +103,16 @@
 
 	if((organ_flags & ORGAN_FAILING) && O.is_drainable() && O.reagents.has_reagent("neurine")) //Neurine fixes dead brains
 		. = TRUE //don't do attack animation.
-		var/cached_Bdamage = brainmob?.health 
+		var/cached_Bdamage = brainmob?.health
 		var/datum/reagent/medicine/neurine/N = reagents.has_reagent("neurine")
 
-		if(O.reagents.has_reagent("mannitol")//Just a quick way to bolster the effects if someone mixes up a batch.
+		if(O.reagents.has_reagent("mannitol"))//Just a quick way to bolster the effects if someone mixes up a batch.
 			N.volume *= 1.5
 
 		if(!O.reagents.has_reagent("neurine", 10))
 			to_chat(user, "<span class='warning'>There's not enough neurine in [O] to restore [src]!</span>")
 			return
-		
+
 		user.visible_message("<span class='notice'>[user] starts to pour the contents of [O] onto [src].</span>", "<span class='notice'>You start to slowly pour the contents of [O] onto [src].</span>")
 		if(!do_after(user, 60, TRUE, src))
 			to_chat(user, "<span class='warning'>You failed to pour [O] onto [src]!</span>")
@@ -123,10 +123,10 @@
 		O.reagents.clear_reagents()
 
 		if(cached_Bdamage) //Fixing dead brains yeilds a trauma
-			if(cached_Bdamage <= HEALTH_THRESHOLD_DEAD && brainmob.health > HEALTH_THRESHOLD_DEAD)
+			if((cached_Bdamage <= HEALTH_THRESHOLD_DEAD) && (brainmob.health > HEALTH_THRESHOLD_DEAD))
 				if(prob(90))
 					gain_trauma_type(BRAIN_TRAUMA_MILD)
-				if else(prob(50))
+				else if(prob(50))
 					gain_trauma_type(BRAIN_TRAUMA_SEVERE)
 				else
 					gain_trauma_type(BRAIN_TRAUMA_SPECIAL)
@@ -136,8 +136,8 @@
 		. = TRUE //don't do attack animation.
 		var/datum/reagent/medicine/mannitol/M = reagents.has_reagent("mannitol")
 		if(brain_death || brainmob?.health <= HEALTH_THRESHOLD_DEAD) //if the brain is fucked anyway, do nothing
-				to_chat(user, "<span class='warning'>[src] is far too damaged, you'll have to use neurine on it!</span>")
-				return
+			to_chat(user, "<span class='warning'>[src] is far too damaged, you'll have to use neurine on it!</span>")
+			return
 
 		if(!O.reagents.has_reagent("mannitol", 10))
 			to_chat(user, "<span class='warning'>There's not enough mannitol in [O] to restore [src]!</span>")
@@ -152,13 +152,13 @@
 		setOrganDamage((damage - (0.05 * maxHealth)*M.volume))	//heals a small amount, and by using "setorgandamage", we clear the failing variable if that was up
 		O.reagents.clear_reagents()
 		return
-	
 
 
-/obj/item/organ/brain/examine(mob/user)//BUG_PROBABLE_CAUSE to_chats changed to . += 
+
+/obj/item/organ/brain/examine(mob/user)//BUG_PROBABLE_CAUSE to_chats changed to . +=
 	. = ..()
 
-	if(suicided)
+	if(user.suiciding)
 		. += "<span class='info'>It's started turning slightly grey. They must not have been able to handle the stress of it all.</span>"
 	else if(brainmob)
 		if(brainmob.get_ghost(FALSE, TRUE))
@@ -247,6 +247,10 @@
 		owner.death()
 		brain_death = TRUE
 
+/obj/item/organ/brain/on_death()
+	if(damage <= BRAIN_DAMAGE_DEATH) //rip
+		brain_death = FALSE
+
 /obj/item/organ/brain/process()	//needs to run in life AND death
 	..()
 	//if we're not more injured than before, return without gambling for a trauma

code/modules/mob/living/brain/life.dm

@@ -20,7 +20,7 @@
 		else if(istype(loc, /obj/item/organ/brain))
 			BR = loc
 		if(BR)
-			BR.organ_flags & ORGAN_FAILING = 1 //beaten to a pulp
+			BR.brain_death = TRUE
 
 /mob/living/brain/proc/handle_emp_damage()
 	if(emp_damage)

code/modules/mob/living/carbon/carbon.dm

@@ -814,7 +814,6 @@
 		reagents.clear_reagents()
 	var/obj/item/organ/brain/B = getorgan(/obj/item/organ/brain)
 	if(B)
-		B.organ_flags & ORGAN_FAILING = FALSE
 		B.brain_death = FALSE
 	for(var/thing in diseases)
 		var/datum/disease/D = thing

code/modules/mob/living/carbon/carbon_defense.dm

@@ -405,16 +405,16 @@
 
 		if(istype(ears) && (deafen_pwr || damage_pwr))
 			var/ear_damage = damage_pwr * effect_amount
-			var/deaf = max(ears.deaf, deafen_pwr * effect_amount)
+			var/deaf = deafen_pwr * effect_amount
 			adjustEarDamage(ear_damage,deaf)
 
-			if(ears.ear_damage >= 15)
+			if(ears.damage >= 15)
 				to_chat(src, "<span class='warning'>Your ears start to ring badly!</span>")
-				if(prob(ears.ear_damage - 5))
+				if(prob(ears.damage - 5))
 					to_chat(src, "<span class='userdanger'>You can't hear anything!</span>")
-					ears.ear_damage = min(ears.ear_damage, UNHEALING_EAR_DAMAGE)
+					ears.damage = min(ears.damage, ears.maxHealth)
 					// you need earmuffs, inacusiate, or replacement
-			else if(ears.ear_damage >= 5)
+			else if(ears.damage >= 5)
 				to_chat(src, "<span class='warning'>Your ears start to ring!</span>")
 			SEND_SOUND(src, sound('sound/weapons/flash_ring.ogg',0,1,0,250))
 		return effect_amount //how soundbanged we are

code/modules/mob/living/carbon/damage_procs.dm

@@ -147,15 +147,15 @@
 	if(O)
 		return O.damage
 
-/mob/living/carbon/adjustAllOrganLoss(amount, maximum)
-	for(var/o in internal_organs)
+/mob/living/carbon/proc/adjustAllOrganLoss(amount, maximum)
+	for(var/obj/item/organ/O in internal_organs)
 		if(O && !(status_flags & GODMODE))
 			continue
 		if(!maximum)
 			maximum = O.maxHealth
 		O.applyOrganDamage(amount, maximum)
 		O.onDamage(amount, maximum)
-		
+
 
 ////////////////////////////////////////////
 

code/modules/mob/living/carbon/life.dm

@@ -49,7 +49,6 @@
 
 //Start of a breath chain, calls breathe()
 /mob/living/carbon/handle_breathing(times_fired)
-	/mob/living/carbon/handle_breathing(times_fired)
 	var/next_breath = 4
 	var/obj/item/organ/lungs/L = getorganslot(ORGAN_SLOT_LUNGS)
 	var/obj/item/organ/heart/H = getorganslot(ORGAN_SLOT_HEART)

code/modules/mob/living/living.dm

@@ -500,10 +500,12 @@
 		mood.sanity = SANITY_GREAT
 		mood.update_mood()
 	//Heal all organs
-	if(internal_organs)
-		for(var/organ in internal_organs)
-			var/obj/item/organ/O = organ
-			O.setOrganDamage(0)
+	if(iscarbon(src))
+		var/mob/living/carbon/C = src
+		if(C.internal_organs)
+			for(var/organ in C.internal_organs)
+				var/obj/item/organ/O = organ
+				O.setOrganDamage(0)
 
 
 //proc called by revive(), to check if we can actually ressuscitate the mob (we don't want to revive him and have him instantly die again)

code/modules/mob/transform_procs.dm

@@ -75,7 +75,7 @@
 		O.setOxyLoss(getOxyLoss(), 0)
 		O.setCloneLoss(getCloneLoss(), 0)
 		O.adjustFireLoss(getFireLoss(), 0)
-		O.setBrainLoss(getOrganLoss(ORGAN_SLOT_BRAIN), 0)
+		O.setOrganLoss(ORGAN_SLOT_BRAIN, getOrganLoss(ORGAN_SLOT_BRAIN), 0)
 		O.adjustStaminaLoss(getStaminaLoss(), 0)//CIT CHANGE - makes monkey transformations inherit stamina
 		O.updatehealth()
 		O.radiation = radiation
@@ -236,7 +236,7 @@
 		O.setOxyLoss(getOxyLoss(), 0)
 		O.setCloneLoss(getCloneLoss(), 0)
 		O.adjustFireLoss(getFireLoss(), 0)
-		O.setBrainLoss(getOrganLoss(ORGAN_SLOT_BRAIN), 0)
+		O.setOrganLoss(ORGAN_SLOT_BRAIN, getOrganLoss(ORGAN_SLOT_BRAIN), 0)
 		O.adjustStaminaLoss(getStaminaLoss(), 0)//CIT CHANGE - makes monkey transformations inherit stamina
 		O.updatehealth()
 		O.radiation = radiation