I am still in the middle of the main quest. Poverty, Chasity, and Obedience. Vashek and Andrew are also hostile to me when I ask them to train me, I saw on the wiki this is a glitch, will this be fixed any time soon?
Friend in need quest should be active right from Awakening main quest, so i am not sure what’s happening there.
If you send me your save i can look in what state the quest is
As for hostile NPCs you can always pop in to church to pay indulgence. That should reset your reputation with all NPCs in the world.