You need the talking tree branch from the Dark Forest, not the one from Mpenzak. If you notice during the ceremony, the fake branch is the only item not to be removed from the pentagram.
When the head of the assassin guild disappeared, he was standing by a cupboard, that had been locked previously...
There is a house crossing the western wall of the quarantine area. I think the back door can be lockpicked, or Lain (IIRC) in the poor quarters has the key (the guy who suggests you join the thieves' guild).
Did you find the cure potions in Elrath's cellar before having him arrested?
