diff --git a/code/ATMOSPHERICS/atmospherics.dm b/code/ATMOSPHERICS/atmospherics.dm
index 4dfe8d70812..a7fe9ddd537 100644
--- a/code/ATMOSPHERICS/atmospherics.dm
+++ b/code/ATMOSPHERICS/atmospherics.dm
@@ -41,11 +41,14 @@ Pipelines + Other Objects -> Pipe network
 	if(!pipe_color_check(pipe_color))
 		pipe_color = null
 
+	..()
+	
+/obj/machinery/atmospherics/initialize()
+	..()
+
 	if(can_unwrench)
 		stored = new(src, make_from = src)
 
-	..()
-
 /obj/machinery/atmospherics/Destroy()
 	for(var/mob/living/M in src) //ventcrawling is serious business
 		M.remove_ventcrawl()
@@ -210,7 +213,7 @@ Pipelines + Other Objects -> Pipe network
 	dir = D
 	initialize_directions = P
 	var/turf/T = loc
-	level = T.intact ? 2 : 1
+	level = T.intact ? 2 : 1	
 	initialize()
 	var/list/nodes = pipeline_expansion()
 	for(var/obj/machinery/atmospherics/A in nodes)
diff --git a/code/ATMOSPHERICS/components/binary_devices/binary_atmos_base.dm b/code/ATMOSPHERICS/components/binary_devices/binary_atmos_base.dm
index b546268b4e0..343501dfd28 100644
--- a/code/ATMOSPHERICS/components/binary_devices/binary_atmos_base.dm
+++ b/code/ATMOSPHERICS/components/binary_devices/binary_atmos_base.dm
@@ -42,6 +42,7 @@
 	return ..()
 
 /obj/machinery/atmospherics/binary/initialize()
+	..()
 	var/node2_connect = dir
 	var/node1_connect = turn(dir, 180)
 
diff --git a/code/ATMOSPHERICS/components/omni_devices/omni_base.dm b/code/ATMOSPHERICS/components/omni_devices/omni_base.dm
index 55216a5a5c2..f1241079ad3 100644
--- a/code/ATMOSPHERICS/components/omni_devices/omni_base.dm
+++ b/code/ATMOSPHERICS/components/omni_devices/omni_base.dm
@@ -57,6 +57,7 @@
 	return ..()
 
 /obj/machinery/atmospherics/omni/initialize()
+	..()
 	for(var/datum/omni_port/P in ports)
 		if(P.node || P.mode == 0)
 			continue
diff --git a/code/ATMOSPHERICS/components/trinary_devices/trinary_base.dm b/code/ATMOSPHERICS/components/trinary_devices/trinary_base.dm
index a008b8886d5..9824715c1f4 100644
--- a/code/ATMOSPHERICS/components/trinary_devices/trinary_base.dm
+++ b/code/ATMOSPHERICS/components/trinary_devices/trinary_base.dm
@@ -67,7 +67,7 @@
 	return ..()
 	
 /obj/machinery/atmospherics/trinary/initialize()
-
+	..()
 	//Mixer:
 	//1 and 2 is input
 	//Node 3 is output
@@ -78,10 +78,6 @@
 	//Node 2 is filtered output
 	//Node 3 is rest output
 	//If we flip the filter, 1 and 3 shall exchange positions
-	
-	if(can_unwrench) // Overridden here to avoid having to snowflake the flipped/icon_state on the construction
-		qdel(stored)
-		stored = new(src, make_from = src) 
 
 	var/node1_connect = turn(dir, -180)
 	var/node2_connect = turn(dir, -90)
diff --git a/code/ATMOSPHERICS/components/unary_devices/unary_base.dm b/code/ATMOSPHERICS/components/unary_devices/unary_base.dm
index 76bd3ddc8c7..15b254093f9 100644
--- a/code/ATMOSPHERICS/components/unary_devices/unary_base.dm
+++ b/code/ATMOSPHERICS/components/unary_devices/unary_base.dm
@@ -23,6 +23,7 @@
 	return ..()
 
 /obj/machinery/atmospherics/unary/initialize()
+	..()
 	for(var/obj/machinery/atmospherics/target in get_step(src, dir))
 		if(target.initialize_directions & get_dir(target,src))
 			var/c = check_connect_types(target,src)
diff --git a/code/ATMOSPHERICS/pipes/cap.dm b/code/ATMOSPHERICS/pipes/cap.dm
index 6f70cf52465..35916a5b575 100644
--- a/code/ATMOSPHERICS/pipes/cap.dm
+++ b/code/ATMOSPHERICS/pipes/cap.dm
@@ -62,6 +62,7 @@
 	overlays += icon_manager.get_atmos_icon("pipe", , pipe_color, "cap" + icon_connect_type)
 
 /obj/machinery/atmospherics/pipe/cap/initialize()
+	..()
 	for(var/obj/machinery/atmospherics/target in get_step(src, dir))
 		if(target.initialize_directions & get_dir(target,src))
 			var/c = check_connect_types(target,src)
diff --git a/code/ATMOSPHERICS/pipes/manifold.dm b/code/ATMOSPHERICS/pipes/manifold.dm
index 555ee66dbfd..6e6a8569ad9 100644
--- a/code/ATMOSPHERICS/pipes/manifold.dm
+++ b/code/ATMOSPHERICS/pipes/manifold.dm
@@ -33,6 +33,7 @@
 	icon = null
 	
 /obj/machinery/atmospherics/pipe/manifold/initialize()
+	..()
 	for(var/D in cardinal)
 		if(D == dir)
 			continue
diff --git a/code/ATMOSPHERICS/pipes/manifold4w.dm b/code/ATMOSPHERICS/pipes/manifold4w.dm
index 8f8b8460486..be0019a43a2 100644
--- a/code/ATMOSPHERICS/pipes/manifold4w.dm
+++ b/code/ATMOSPHERICS/pipes/manifold4w.dm
@@ -152,6 +152,7 @@
 	update_icon()
 
 /obj/machinery/atmospherics/pipe/manifold4w/initialize()
+	..()
 	for(var/D in cardinal)
 		for(var/obj/machinery/atmospherics/target in get_step(src, D))
 			if(target.initialize_directions & get_dir(target,src))
diff --git a/code/ATMOSPHERICS/pipes/simple/pipe_simple.dm b/code/ATMOSPHERICS/pipes/simple/pipe_simple.dm
index 7908acc5321..c3d1762b993 100644
--- a/code/ATMOSPHERICS/pipes/simple/pipe_simple.dm
+++ b/code/ATMOSPHERICS/pipes/simple/pipe_simple.dm
@@ -44,6 +44,7 @@
 			initialize_directions = SOUTH|WEST
 		
 /obj/machinery/atmospherics/pipe/simple/initialize()
+	..()
 	normalize_dir()
 	var/N = 2
 	for(var/D in cardinal)
diff --git a/code/game/machinery/pipe/construction.dm b/code/game/machinery/pipe/construction.dm
index 667602686b5..47bbfa2715f 100644
--- a/code/game/machinery/pipe/construction.dm
+++ b/code/game/machinery/pipe/construction.dm
@@ -164,7 +164,7 @@
 			src.color = PIPE_COLOR_RED
 		else if (pipe_type == PIPE_UNIVERSAL)
 			connect_types = list(1,2,3)
-	//src.pipe_dir = get_pipe_dir()
+
 	update(make_from)
 	src.pixel_x = rand(-5, 5)
 	src.pixel_y = rand(-5, 5)
@@ -275,14 +275,8 @@
 
 	src.dir = turn(src.dir, -90)
 
-	if (pipe_type in list (PIPE_SIMPLE_STRAIGHT, PIPE_SUPPLY_STRAIGHT, PIPE_SCRUBBERS_STRAIGHT, PIPE_UNIVERSAL, PIPE_HE_STRAIGHT, PIPE_INSULATED_STRAIGHT, PIPE_MVALVE, PIPE_DVALVE))
-		if(dir==2)
-			dir = 1
-		else if(dir==8)
-			dir = 4
-	else if (pipe_type in list (PIPE_MANIFOLD4W, PIPE_SUPPLY_MANIFOLD4W, PIPE_SCRUBBERS_MANIFOLD4W))
-		dir = 2
-	//src.pipe_dir = get_pipe_dir()
+	fixdir()
+
 	return
 	
 /obj/item/pipe/verb/flip()
@@ -406,22 +400,6 @@
 
 //Helper to clean up dir
 /obj/item/pipe/proc/fixdir()
-	if (pipe_type in list (PIPE_SIMPLE_STRAIGHT, PIPE_HE_STRAIGHT, PIPE_INSULATED_STRAIGHT, PIPE_MVALVE, PIPE_DVALVE))
-		if(dir==2)
-			dir = 1
-		else if(dir==8)
-			dir = 4
-
-/obj/item/pipe/attack_self(mob/user as mob)
-	return rotate()
-
-/obj/item/pipe/attackby(var/obj/item/weapon/W as obj, var/mob/user as mob, params)
-	..()
-	//*
-	if (!istype(W, /obj/item/weapon/wrench))
-		return ..()
-	if (!isturf(src.loc))
-		return 1
 	if (pipe_type in list (PIPE_SIMPLE_STRAIGHT, PIPE_SUPPLY_STRAIGHT, PIPE_SCRUBBERS_STRAIGHT, PIPE_HE_STRAIGHT, PIPE_INSULATED_STRAIGHT, PIPE_MVALVE, PIPE_DVALVE))
 		if(dir==2)
 			dir = 1
@@ -429,13 +407,27 @@
 			dir = 4
 	else if (pipe_type in list(PIPE_MANIFOLD4W, PIPE_SUPPLY_MANIFOLD4W, PIPE_SCRUBBERS_MANIFOLD4W, PIPE_OMNI_MIXER, PIPE_OMNI_FILTER))
 		dir = 2
+
+/obj/item/pipe/attack_self(mob/user as mob)
+	return rotate()
+
+/obj/item/pipe/attackby(var/obj/item/weapon/W as obj, var/mob/user as mob, params)
+	..()
+
+	if (!istype(W, /obj/item/weapon/wrench))
+		return ..()
+		
+	if (!isturf(src.loc))
+		return 1
+
+	fixdir()
+		
 	var/pipe_dir = get_pipe_dir()
 
 	for(var/obj/machinery/atmospherics/M in src.loc)
 		if((M.initialize_directions & pipe_dir) && M.check_connect_types_construction(M,src))	// matches at least one direction on either type of pipe
-			user << "\red There is already a pipe of the same type at this location."
+			user << "<span class='warning'>There is already a pipe of the same type at this location.</span>"
 			return 1
-	// no conflicts found
 
 	var/obj/machinery/atmospherics/machineReference = null //If somebody wants to overhaul that switch statement below, be my guest. Easier to set a reference here and then transfer logs after the switch statement.
 
@@ -603,11 +595,6 @@
 	qdel(src)	// remove the pipe item
 
 	return
-	 //TODO: DEFERRED
-
-// ensure that setterm() is called for a newly connected pipeline
-
-
 
 /obj/item/pipe_meter
 	name = "meter"