After making lot of progress, I’m took a small break from City of Tears in light of discovering a problem with its connection to Crossroads by the elevator, so I decided to take some preemptive steps to prevent that kind of problem in the future.
Because of a sudden realisation I made after I have inserted the almost-finished City of Tears into the world map (namely that the lift shaft between the City and Crossroads didnt meet), I accepted that the only way to avoid this kind of problem is to go and quickly assemble all the areas take screenshots of all the areas and roughly assemble them, to see where I need to make adjustments. In order for certain connections between areas to be aligned while making sure other connections to all areas involved also remain aligned, I will need to make some adjustments within the area itself, which is a preferable solution over adding very long tunnels to make “ends” meet.
For example, you can see in this image that Fungal Wastes has a lot of blank space around it, because other areas have vertical connections to further-away areas. To combat this, after finishing City of Tears, I will focus on coming up for solutions to all of these blank spaces, simply by identifying which chunk of each area needs moving towards what direction, making sure I’m not breaking perfectly aligning connections.