I’m guessing you used the “erect walls” command for this floor plan (for the outer/main walls)? I know it’s a pain, but what if you try drawing every single wall out by hand, then building the floors around them? I did it before with the Fort Lias Cathedral for the corner bedrooms, and the hearthlings seemed to use the rooms and beds fine. Somehow, the individual wall plan doesn’t mess up the pathfinder with “internal” doors, I believe.
See if it works for you! I might try and do a little experimenting myself this weekend, see if I can’t come up with a new project myself.