When mapping large areas like this, it's important to decide exactly how much detail is worth showing, and what the map is going to be used for (both of which go hand-in-hand).

A settlement will always require farmlands of some kind nearby, so any settlement means there will be such areas around it, even where the map doesn't show them. Then you can use the actual farmland areas to show those places that are particularly important farming areas - key places that the whole country/nation may rely upon, for instance. There, you wouldn't need to show any but the larger or most significant settlements (e.g. like the hamlet the party will be starting from!); all the other hamlets and villages can be assumed as present scattered among the farmland region without you needing to show each one.

For the non-cliff coastlines, I'd be inclined to soften the edges somewhat, maybe with a small Edge Fade effect, or reintroduce the "coastline" blue line for them. Softening the land edges on the cliff coasts wouldn't go amiss either, perhaps.

The aerial floating island looks interesting. Depending on how your floating lands like this work, you might also consider adding some crystal symbols (e.g. from one of the Dungeon sets, suitably enlarged of course!), or by using varicolor mountain symbols. With the settlement on top, it may be worth placing that directly onto the rocky mountain symbols, or with only a much smaller area of grassland fill texture behind the settlement image, then using just the mountain symbols (probably on their own, new Sheet) to cast a suitable drop-shadow. If the grass needs to definitely run right to the very edge of the stony platform, maybe make that more ragged, to closely match the symbol lines underneath indicating where that edge is.

For the Church, the pillar shadows could use some adjustment, as right now, they're passing over and through the walls, which is confusing.

On the upper floor (which might benefit from labelling as such), the stained-glass window patterns thrown on the floor need adjusting, so they cover only where the wooden flooring is - where they shine into the air beyond, there should be nothing.

Additionally, not all the windows should be showing these at all on either floor, only where the light will be shining directly through them, and that should match with where the floor shadows lie as well.

It might be helpful to add dashed or transparent lines on the lower floor image to indicate where the upper balconies are on the lower map view.

You could try adding a new polygon of the surface fill texture above the hedges sheet, but below the cliff symbols sheet. You'd have to draw it either exactly along the outside of the hedge symbols to retain the impression and hide the hedge shadows, or draw it quite close to them, so only part of the shadow is still visible, however. The latter might look a bit oddly sharp-edged though.

So alternatively, you might try moving the problematic hedge symbols to a new sheet with a smaller shadow effect, suggesting they're closer to the rising lower hill surface behind the cliff-line.

You could also redraw the cliff line as shorter and lower, so the hedge shadows aren't so obviously problematic.

Certainly, I found drawing "Naughty Lass" quite a challenge overall. There's a particular complexity in trying to visualise things in 3D to be able to draw 2D versions from top-down and side-on viewpoints, and deciding exactly which line you'll pick for the cross-section, etc. There isn't an ideal solution, so you end up just picking whatever seems to work better, and hope users/viewers will be able to tell what was intended.

There is a similarity to the cross-sectional views of caves we've discussed before here, though with a ship, you can't usefully vary the line of any sections, as that just makes it still harder to draw for a vehicle.

I'm not saying it will definitely help, as I'm not sure what changes were made when the Ships Annual was updated, as they were drawn only using the original, but I had to handle similar deck-level elements, and other features, when designing "The Naughty Lass" for the Atlas. For ease, you can pick up the deck plans FCW here, and the sideview here, in case those may assist.

Note though that I did "cheat" with the yards, by having them piercing their respective masts, partly because it's a magical vessel, partly because I was trying to avoid needing to show the complexities of the rigging...