I finally created a working level builder, how it works:

1. elevator screen calls level builder to build level from asset,
2. it sets up the bounds (for putting the tiles into a non-negative position),
3. it adjusts the tiles from the asset,
4. it places the areas, rooms, and the exits,  then makes them comply with the bounds,
5. it places the tiles based off a list, then textures the tiles
6. it places the items and the notebooks, then makes them comply with the bounds.
7. It places the objects based off the tile from the list (the plants, the tables, etc), then they are put into the tile.
8. it places the tutor Noisious,
9. it places the wander points,
10. it sets up the NavMesh,
11. it places the NPCs based off a list of Vector2s.