There are 2 cure potions in Elrath's cellar that you need to cure the 'plague' victims. The smelly flasks were how the doctor brought the poison there. His door can not be lockpicked once he is arrested, but you can get back in;
FIX for the Missing Catacombs Portal or
Teleporting Anywhere, via hex editoror you may be able to stand at the north west corner of the house and toss a teleporter stone through the wall into the front room.
or get the potions directly;
Lost Items - guide and directory of inventory filesWhen 2 people are cured, you can Pickpocket (level 2) a potion back to give to the third person, or kill one of them (no reputation drop). Alternately, when you have both potions, you can cheat to duplicate them;
Drag a stack out of (or into) your inventory (or container) and hold down the control key before dropping. This will bring up the split stack pane; type in a negative number and hit enter (the checkmark will be greyed out). This can also be done in the trade window.
The holy sword is on the first level of Iona's dungeon. Go back through the graveyard entrance, and in the north central area of that level there is a corridor you can see, with a wall blocking the way. South of there is a skeleton with a candle in a pentagram. Light the candle...
The amulet was from the cave in the Dark Forest where you got the vase for the collectors.
There is a book in the cursed abbey warning not to touch the tombs in the place of sacrifice, but it is not required.
Help! Can't find Gyrion... Iona's dungeon maps
To find Shrimpo, check out the tombstones in the north east area of the cemetery (the only ones you can read). Click on them so that the first letter of each name spells out 'SHRIMPO'.
You need level 5 Lockpick IIRC to open the cell that has the map.