Mission 4: The Royal Physician
When you get across the tracks, drop down to the road and go down the alley. Behind the building there, blink up to the balcony above and the rune will be in the doorway there.
As soon as you enter drawbridge control, steal the key from Pratchett or kill him and enter his house on the left side. Look at the paintings on each floor for the numbers needed and then enter 473 on the safe to open it and grab the rune.
Rune 4-3 / Outsider Shrine 4-1
Exit the balcony to the right of the safe in Pratchett’s house and blink to the balcony across the way. Blink again to the next balcony on the right and enter the apartment there. Go around the right corner to find the Outsider Shrine and the rune on it.
As soon as you enter Midrow Substation after disabling the drawbridge lights, the rune will be on a desk directly in front of you.
When you reach Sokolav in his greenhouse above his place, the rune will be on the left side of the room on a desk.