Sorry I don't think I'm going to be of much help for troubleshooting, I don't really have any experience in this particular application. I feel like in a bit of an awkward place, like a beginner giving advice to an expert ><
I hadn't thought about pathfinding, that is going to be quite a lot of work! Even regardless of multiplayer, I don't think there are any easy ways about having multiple floors with pathfinding... Maybe might be of use? Run pathfinding per floor via tilemap, at least to the "exit" or "stairs" to the next floor.