I have the same problem. I am playing on tactician difficulty, but there's no Malady and no Jahan and the Doctor keeps adressing me as "Lohse" (Who died on the Lady Vengeance after act 1) The barrel that you are supposed to use to get into jail seems bugged and I can only loot it and not do anything else with it.
Now I can't progress because he has easily over 25k armor and shield and even more health..
