Singo;
It is best to do all three quests before entering the castle. I did the majority of stuff in Rivertown and Verdistis and cleared the Rivertown sewers before entering the castle, and didn't have any problems with the area afterwards. Some people also recommend doing some of the Dark Forest first, as well.
The army quests can actually be done without much killing. You can use either shadow potions, the survivor's sneak special move or a spider statuette to bypass the orcs and just drop the explosives and poison where they need to go.
Wytse;
You only get one wish each game. The 'come back in 300 years' comment is a round about way of saying no.
the Wishing Well (Spoiler)The holy dagger is in the thieves' guild in Verdistis (Ducal inn cellar), so you need to join to get it.
The entrance to the crypt is just north east of the church (which is north of the cursed abbey), mostly hidden in a small group of trees / brush.