I still don't know why my nav mesh was disappearing on me before, but it is staying now anyway. Here is my homework, let me know if you need more nav mesh pics? I have a screen shot from under the house for the bottom floor, as it was hard to get good viewing angles without including a ton of pics. I also tested the house with a follower to tweak anything wonky, and ended up taking some of the plates away from the table settings, as they were just so wobbly unless the food was perfectly balanced. The only glitchiness I still have is that when someone sits at one table, all the forks on both tables like to immediately fall through onto the floor. I think maybe raising them off the table slightly more might fix that though.
Nav Mesh:
Books, Wine, Ingredients, etc:
Door: (and my character who can't let go of the fact she can be leader of everything in Skyrim, except the Bard's College..)
Second Custom Container:
Place Settings: (Forks intact. Scared away the customers though... )
All forks now on the floor..