Now working, let's do this

code/controllers/subsystem/shuttles.dm

@@ -14,6 +14,7 @@ var/datum/subsystem/shuttle/SSshuttle
 
 	var/list/turf/transit_turfs = list()
 	var/list/transit_requesters = list()
+	var/clear_transit = FALSE
 
 		//emergency shuttle stuff
 	var/obj/docking_port/mobile/emergency/emergency
@@ -66,6 +67,7 @@ var/datum/subsystem/shuttle/SSshuttle
 	var/turf/B = get_turf(transit_markers[2])
 	for(var/i in block(A, B))
 		var/turf/T = i
+		T.ChangeTurf(/turf/open/space)
 		transit_turfs += T
 		T.flags |= UNUSED_TRANSIT_TURF
 #ifdef HIGHLIGHT_DYNAMIC_TRANSIT
@@ -75,10 +77,16 @@ var/datum/subsystem/shuttle/SSshuttle
 			T.color = "#00ffff"
 #endif
 
-	world.log << "[transit_turfs.len] transit turfs registered"
+	//world.log << "[transit_turfs.len] transit turfs registered"
 
 /datum/subsystem/shuttle/fire()
-	if(transit_requesters.len)
+	if(clear_transit)
+		transit_requesters.Cut()
+		for(var/i in transit)
+			qdel(i, force=TRUE)
+		setup_transit_zone()
+		clear_transit = FALSE
+	else if(transit_requesters.len)
 		var/requester = popleft(transit_requesters)
 		var/success = generate_transit_dock(requester)
 		if(!success) // BACK OF THE QUEUE
@@ -254,20 +262,25 @@ var/datum/subsystem/shuttle/SSshuttle
 	// Because of shuttle rotation, the "width" of the shuttle is not
 	// always x.
 	var/travel_dir = M.preferred_direction
-	//var/coords = M.return_coords(0, 0, travel_dir)
+	var/dock_angle = dir2angle(M.preferred_direction) + M.port_angle + 180
+	var/dock_dir = angle2dir(dock_angle)
 
-	var/transit_width = 14
-	var/transit_height = 14
+	var/transit_width = SHUTTLE_TRANSIT_BORDER * 2
+	var/transit_height = SHUTTLE_TRANSIT_BORDER * 2
 
 	// Shuttles travelling on their side have their dimensions swapped
 	// from our perspective
-	switch(travel_dir)
+	switch(dock_dir)
 		if(NORTH, SOUTH)
 			transit_width += M.width
 			transit_height += M.height
 		if(EAST, WEST)
 			transit_width += M.height
 			transit_height += M.width
+/*
+	world << "The attempted transit dock will be [transit_width] width, and \
+		[transit_height] in height. The travel dir is [travel_dir]."
+*/
 
 	// Then find a place to put the zone
 
@@ -291,33 +304,75 @@ var/datum/subsystem/shuttle/SSshuttle
 				continue
 			for(var/j in proposed_zone)
 				var/turf/T = j
+				if(!T)
+					continue base
 				if(!(T.flags & UNUSED_TRANSIT_TURF))
 					continue base
-			break
+			world << "[COORD(topleft)] and [COORD(bottomright)]"
+			break base
 
 	if((!proposed_zone) || (!proposed_zone.len))
 		return FALSE
 
 	var/turf/topleft = proposed_zone[1]
+	world << "[COORD(topleft)] is TOPLEFT"
 	// Then create a transit docking port in the middle
-	var/mid_x = 7 + M.dwidth + topleft.x
-	var/mid_y = 7 + M.dheight + topleft.y
+	var/coords = M.return_coords(0, 0, dock_dir)
+	world << json_encode(coords)
+	/*  0------2
+        |      |
+        |      |
+        |  x   |
+        3------1
+	*/
 
-	var/turf/midpoint = locate(mid_x, mid_y, topleft.z)
+	var/x0 = coords[1]
+	var/y0 = coords[2]
+	var/x1 = coords[3]
+	var/y1 = coords[4]
+	// Then we want the point closest to -infinity,-infinity
+	var/x2 = min(x0, x1)
+	var/y2 = min(y0, y1)
+/*
+	var/lowx = topleft.x + SHUTTLE_TRANSIT_BORDER
+	var/lowy = topleft.y + SHUTTLE_TRANSIT_BORDER
+
+	var/turf/low_point = locate(lowx, lowy, topleft.z)
+	new /obj/effect/landmark/stationary(low_point)
+	world << "Starting at the low point, we go [x2],[y2]"
+*/
+	// Then invert the numbers
+	var/transit_x = topleft.x + SHUTTLE_TRANSIT_BORDER + abs(x2)
+	var/transit_y = topleft.y + SHUTTLE_TRANSIT_BORDER + abs(y2)
+
+	var/transit_path = /turf/open/space/transit
+	switch(travel_dir)
+		if(NORTH)
+			transit_path = /turf/open/space/transit/north
+		if(SOUTH)
+			transit_path = /turf/open/space/transit/south
+		if(EAST)
+			transit_path = /turf/open/space/transit/east
+		if(WEST)
+			transit_path = /turf/open/space/transit/west
+
+	//world << "Docking port at [transit_x], [transit_y], [topleft.z]"
+	var/turf/midpoint = locate(transit_x, transit_y, topleft.z)
+	if(!midpoint)
+		return FALSE
+	//world << "Making transit dock at [COORD(midpoint)]"
 	var/obj/docking_port/stationary/transit/new_transit_dock = new(midpoint)
 	new_transit_dock.assigned_turfs = proposed_zone
 	new_transit_dock.name = "Transit for [M.id]/[M.name]"
+	new_transit_dock.turf_type = transit_path
 
-	var/dock_angle = dir2angle(M.preferred_direction) + M.port_angle + 180
 	// Add 180, because ports point inwards, rather than outwards
 	new_transit_dock.setDir(angle2dir(dock_angle))
 
 	for(var/i in new_transit_dock.assigned_turfs)
-		var/turf/open/space/transit/T = i
+		var/turf/T = i
+		T.ChangeTurf(transit_path)
 		T.flags &= ~(UNUSED_TRANSIT_TURF)
-		T.ChangeTurf(/turf/open/space/transit)
-		T.setDir(travel_dir)
-		T.update_icon()
 
 	M.assigned_transit = new_transit_dock
 	return TRUE