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

Transparency acne (the pitting) happens when the same or similar textures are used on top of one another on different sheets and the overlying sheet has either an Edge Fade Inner or one of the bevels on it. The rendering engine finds the edges of the polygon on the topmost of the two sheets by comparing the pixels with those underneath it. Where those pixels are the same it interprets an edge. So if the pixel in the top polygon is the same colour as the underlying one the rendering engine sees a pinhole, and will apply the sheet effects to the edges of that hole. It looks particularly bad with this texture because there is quite a pronounced bevel effect on the upper sheet, which is being applied to all those little pinholes right across the polygon.

The reason these pinholes tend to shift around as you zoom in and out is because CC3 is switching between the different resolutions of the textures and the pinholes will appear in different places on the different resolutions where different pixels suddenly match colour and others become different again.

The copy polygon is a backing sheet to separate those two to make sure the pixels don't match. Normally, and logically, you then use change properties on that copy to make sure it's a different colour so that none of the pixels match, but sometimes a straightforward copy is all it takes

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.

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 :)

Let me see what I can do with varicolour first.

I also need to remember that I need to do more Creepy Crypt stuff! LOL!