I made a topic for fixing the quests for certain quest items:
http://www.gamesas.com/index.php?/topic/1296124-placeholder-bug-fix-found-quest-items-before-the-quest-itself-read-on/
Well, this work around, worked for me.
I was able drop the Quest Item from my inventory.
As soon as I picked it up, The Quest update message appeared,
and I was able to finish the quest.
Concerning the other quest that cannot be activated;
"Talk to "So-an-So" (I figured this NPC died) *shrug*
I used the console command
place.playeratme NPC-BaseID
And Voila, the NPC spawned in front of me at the Whiterun Stables,
and started heading down to the roadways.
I'm guessing he was heading back to his town.
I talked to him, and the Quest was updated.
I guess NPC's will die from time to time, mid-quest, but maybe the
Quest Journal should reflect this somehow.
Maybe an option to Remove the Quest.
Anyways, nice workaround.
Console players will still have these issues though, since no access to the cmd line.