I haven't destroyed that one room with 3 coffins. Do all three coffins have a backlog of every dead character? Or do they disappear with time?
I think one coffin is one dead character. If you anticipate more death, you need more rooms and more coffins.
Also, is there any suggestions for an ideal layout of brothel and dungeon itself? Or am I just gonna have to accept the fact that whatever layout for the rooms I come up with is going to be a chaotic mess?
I lay out my dungeon in a pattern:
monster cage | breeding cage | birth room | milking room | slave cage
For big monsters, slave cage can be put below the birth room and milking room. An extra monster cage helps too.
The idea is to have each such floor operate in a more-or-less self-contained manner, reducing chaos.
Eventually, I have to re-design the top few floors to support the brothel. Birth rooms, milking rooms, slave cages for newborns. Many slave cages for newborns, because new slaves seem to be constantly overflowing and clogging up everything.
To the left and right of the main floors, I can arrange tentacle rooms and training rooms. They don't need to be anywhere specific, but training rooms tend to get clogged up because newly trained slaves have their places in cages take up by newborns.
I try to arrange brothel in a meaningful way too, but I have yet to find a good way to do it. My brothel is usually a mess of breeding projects, especially if I'm using Complex Breeding.
But how do I get the harem endings within a 50 day timeframe as quickly as possible?
Most of your colleagues' desires can be fulfilled by throwing money at them. Start by focusing on earning a lot of money and diversifying your establishment, you'll fulfill many of their requirements automatically. Once you're confident in your funds, start methodically doing what needs doing. Like, build a huge number of rooms for Barbara to upgrade (you don't have to actually use them). Buy slaves of different races and send them to be slaughtered (descendants of special slaves and brainwashed colleagues are better for actually working in your establishment).
Don't forget you can ask the slave dealer to change her stock at any time, you don't need to wait a whole day.
Laboratory is the only place with severe time constraints. Upgrade speed to the maximum. Breed human slaves and goblin monsters - at max upgrade they spawn instantly. So you'll only need to wait for your third big monster (you should have already got 2 others by this point).