There are several ready made projections available in the March issue of the 2014 Cartographer's Annual if you have it (you get to them by opening a new overland map and selecting "Pick a pre-defined template"), but none of them are Wagner VII.

Well done - a beautiful map :)

When I opened your map I saw the pits as you described them

I copied the pitted polygon to the WATER sheet by right clicking the hourglass and using the "Copy to sheet" option to copy it to the WATER sheet.

And got this result.

All it does is add a backing to the overlying polygon to separate it from the underlying one. Normally you have to then go and change the copy to be a solid colour that isn't in the texture, but it seems to work fine without that.

I think the only person who can answer that is currently on holiday ;)

Cities come in all shapes and sizes. I suppose realism is down to where you put the city centre and all the important and functional buildings.

I chose to stick with Imperial ;)

Looks good, but you've got a touch of transparency acne on those topmost wall sections. You can cure that by copying them onto a new sheet directly below and changing the fill of the copies to solid and any colour that isn't in that fill. 227 is a good one.

Looks good to me :)

I think it looks fine as it is, but you may be right about the docks. It would be a pity to build a city divided into 3 sections like that by water, and have no dock in sight.

Decision time, then. We can't help you make the decision, but it might help you if you do a blank Watabou and Fantasy Cities map of the correct size and just dot a single housing estate and a few trees on it to see what they look like when rendered to the correct size.

What happens if you create a new map in the style and paste the bushes?