I don't understand...you done with the quests and they still marked??
I'm just writing some stuff maybe it will help you.
*closing the rift aka The Shelter Plane attack is in Luculla forest in the lava area. there is a blood stone that you need to destroy to complete this quest.
*Weresheep - optional , near the end of the game.
put stardust plant near the tree next to the Cassandra area
*Fredrick and the imp...hmm I help Fredrick and killed him, after that I found the Imp and help him with scourge potion...he saw that Fredrick is dead and the quest marked as complete.
*war of stones - just kill all the orcs.
*The initiation- hmmm...yep you killed him
hmmm if you say that you require more bloodstones try to hunt them using this list:
1 - Doctors office - make a choice
2 - Ransacked inn room
3 - Black cove pirate treasure box
4 - Braccus's Rex tomb
5 - N exit from first area (fire zone)
6 - Hiberium prison inside an iron maiden (destroy it)
7 - King Boreus Treasure room
8 - Immaculate trial stone
9 & 10 - Basement of the immaculte church
11 - Totem in the goblem village (destroy it)
12 - Marando one (inside his hidden place, its a shard but works the same)
13 - Knights tomb E of hunters edge
14 - In the statue behind cassandras remains
15 - Source temple behind a mirror
16 - Immaculate trial area (cassandra's blood dungeon)
