Clicking on the gong should ring an alarm, so that 3 of the 4 guards in the next room run to the gong room, and 1 to the room north of there. That will let head back west, then north, and just fight 1 guard to get to Samuel's lair. You can also first take out the other 3 guards (rather than all 4 at once).
There was a book near the start of the game describing how to make gunpowder. If you combine coal (Furgus' room), salt (citadel kitchen) and then sulphur (gay medic's room) to make a bomb, you can drop it onto the forge to flood the citadel and move to the next act (unlike leaving by the stairs, this gives experience points).
The cook should have mentioned not being able to start a meal due to rats in the storage room, and asked you to tell the imp to get rid of them. The imp is hiding south of the kitchen, and will ask you to kill the rats for him. If you agree, you will get the key to the storage room (not much there), if not you can tell him to go himself, in which case he will die.
