A very very easy way to kill him is if you have an archer, use haste, then shoot him point blank with 'arrow spray'. When the fight start you should get a free turn from the haste. Which should kill him in his human form.

Another easy way to kill him is to have someone sneak behind the doctor in stealth, damage him and start the battle. Try to take out all his physical armor before your turn is up. Use Forced Exchange (you need the stealth character to be really low on health) and boom. Dead.

A super duper fool proof way to kill him is throw a death fog crate at him..... Boom?

So Malady should be waiting at the Black House? or will she only be there if you have Lohse with you

I like how he randomly calls me Fane when we first meet, then he proceeds to call me Lohse after I refuse his deal... Neither of those characters are in my party

Is there something to do at the end of the cellar where all the fish are?

I did a save reload during the fight (I had snuffed out the candles) and the doctor had been reduced to just under four thousand health and less than that in both types of armour.

Accidentally killed him by going into sneak with Lohse, which made his turns go away.

Huuuh, there is no Lahan in jail for me, nor Malady.
In jail, I get the dwarf bard from Driftwood, the poor thing wasn't in good state.
So for Lahan I guess that's because I killed the guys that the Advocate wanted dead while I didn't even encountered the Advocate at this time ( killed it right after, then reported the name to Jahan ). I guess that messed with this(?).
For malady and all this Demon's Dimension I guess it's all with Lohse quest, not the " Doctor's Order " quest itself (?).
Also, this quest is certainly the worst designed quest I did, opponent calling you randomly Fane or Lohse even without them in your party...