Tried to fix the amputee pain problem.

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

@@ -22,7 +22,7 @@
 		var/mob/living/carbon/human/M = src
 		for(var/name in M.organs)
 			var/datum/organ/external/organ = M.organs[name]
-			if(organ.status & DESTROYED)
+			if((organ.status & DESTROYED) && !organ.amputated)
 				src.traumatic_shock += 60
 			else if(organ.status & BROKEN || organ.open)
 				src.traumatic_shock += 30

code/modules/mob/new_player/preferences.dm

@@ -1223,6 +1223,7 @@ datum/preferences
 
 			var/status = organ_data[name]
 			if(status == "amputated")
+				O.amputated = 1
 				O.status |= DESTROYED
 				O.destspawn = 1
 			else if(status == "cyborg")

code/modules/mob/organ/organ.dm

@@ -97,6 +97,7 @@ var/list/wound_progressions = list(
 	var/tmp/perma_injury = 0
 	var/tmp/perma_dmg = 0
 	var/tmp/destspawn = 0 //Has it spawned the broken limb?
+	var/tmp/amputated = 0 // Whether this has been cleanly amputated, thus causing no pain
 	var/min_broken_damage = 30
 
 	var/datum/organ/external/parent

code/modules/mob/organ/pain.dm

@@ -55,6 +55,9 @@ mob/living/carbon/human/proc/handle_pain()
 	var/datum/organ/external/damaged_organ = null
 	for(var/name in organs)
 		var/datum/organ/external/E = organs[name]
+		// amputated limbs don't cause pain
+		if(E.amputated) continue
+
 		var/dam = E.get_damage()
 		// make the choice of the organ depend on damage,
 		// but also sometimes use one of the less damaged ones