If it is just things getting to dark in the shadows, maybe consider just lowering the opacity of the Wall Shadow effect instead of trying to add point lights?

The point light system is a completely different way of creating shadows, and doesn't work with the well shadow effect. Which means that if you want to use it, you can't just set up a light source in the dark corner, you have to properly set up lighting for the entire room.

Am I understanding you right here that each sheet is one floor, so that all the floors are in the same map file?

In CC3+, because of things like sheets effects and such, maps tends to use a lot of sheets, so it is generally better to use one map per floor. Although it is possible to keep it as one map too, but then the macros hiding the sheets must be updated to hide the complete set of sheets. With some nice naming you can do this rather easily by taking advantage of the HIDESHTF and SHOWSHTF commands which hides and show sheets by a wildcard filter, so for example all sheets for floor 1 could be named FLOOR1_SOMETHING and so on.

If you're looking for something in particular, the atlas is fully searchable, although there are no search option for interesting locations though.

To pick a spot, find some feature on any map that looks like it could hold a dungeon. Could be a cave, or a ruin, or a building (both on the overland map or a city map)), or perhaps there are some stairs or holes in another dungeon out there that may lead to yours?

And note that the mega-dungeon always could use new levels. It is already a crazy place with levels completely different from each other, making it a good place for anyone just wanting to make a dungeon level without looking for a specific location in the atlas (Just remember that mega-dungeon levels should have exactly one entrance from above and one exit going down so they can be linked in a long chain.)

a) This is a bug that happens rarely, but do show up every now and then. The fastest way to fix it is to just use :CC2KEEP: on the existing wall, the erase it, and then draw a new one with the :CC2PATH: tool. Note that the dungeon corridor tool adds a little notch of wall at the end there, overlapping the meeting perpendicular wall, this is to get a full corner there.

b) Not sure. I didn't have any problems at all placing a door and cutting the room there once I turned off snap. If you have trouble with the behavior though, the workaround is to :CC2BREAK: the wall manually instead. (Hide the floor first to make sure you work with the right entity)

Well, that's the problem then. Just move the COASTLINE sheet upwards to right between RIVERS and ROADS, which is where it is supposed to be.

What probably happened here is that the COASTLINE sheet was missing from the template you used, which caused CC3+ to automatically created it when it was needed for that outline. But CC3+ don't know where in the order to put such a automatically created sheet, so it just puts it on top of everything.

Edit: And a fast Lorelei sneaks in......