OK! So, with comic0062's help and collaboration, I went and remade the floorplan.
Instead of ripping my hair out any further, we decided instead on ignoring several major inconsistencies and just— just go for it. So some parts are made up to fit into the general shape of the Mystery Shack. I figure, especially with the earlier episodes, they’re still getting their… stuff together and consider any further information/latest episodes to be most canonical in that regard.
At least, I’m finally relieved to get this out of my system.