For 2) If you don't mind a long fic:
Into Your Hideaway (http://archiveofourown.org/works/1069692/chapters/2146371) (Dean/Cas)
On the Road Again (http://archiveofourown.org/works/1432147/chapters/3011266) (Dean/Michael initially, Dean/Cas at the end)

For 3)
To Know You and Be Known (http://archiveofourown.org/works/2645207) (Dean/Cas and It's not so much John hunting Dean as it is Dean dealing with the abuse John put him through for years because he believed Dean was a monster)
See Spot Run (http://archiveofourown.org/works/174496) (Skinwalker!Dean and John is hunting down all the skinwalkers because he thinks Dean was killed by one, also Bobby finds Dean and raises him)