Chamber of Strategy
It seems the solution could use more work and probably reworked in the format, from what I've noticed the solution is different per save file, so far there's 2 types and not sure if there's a 3rd or 4th and I still don't know what insitgates the puzzle to choose one of the two. (Does it happen when that area is loaded first time? or when you step into rivington?)
The easiest way to solve this is having Gale in your party. He will give the solution when talking to him.
Chamber of Justice
You can cast lv4 spell 'Banishment' on shadow to remove him as well.
Command: Flee does NOT work on undead (tested in Honour mode, idk if that matters?)