#1) This Rune is located in the Greaves Refinery area, which is the area where you go to get your gear back. It is on the ground, outside of the building where your gear is located, hidden in the bushes.
#2) This one is located in the Central Rudshore area. After stealing Daud's key, you will need to head to a door far below you that you get to by climbing down a chain. The Rune is right there at the bottom of the chain.
#3) This Rune is located in the Gateward Tunnel area. You can get inside the second to last building before the train tracks (two balconies, you want the first balcony). The window in this building is connected to the adjacent one with a ramp. Keep going back and forth between these two buildings until you come out a window and onto the rooftops. The Rune is located on the highest rooftop you can climb to, right in the open.
#4) In the room where you confront Granny Rags and Slackjaw, go upstairs and into the bedroom. There's a door up here that leads to some stairs, where the Rune is resting on an Outsider Shrine.
#5) This Rune is located in the sewers section of the Old Port District area. When you reach the area with the Weepers/Survivors (High/Low Chaos respectively), the Rune is underneath the walkways there.
