The water lines problem looks to be one of the classic issues with too many nodes too close together, in this case because the water drawing tool is set to not extend beyond the map border, and as a smooth drawing tool, it will automatically put a pair of "Corners" at the map border to create the straight line there. A Corner is basically three nodes very close together.

A quick check suggests you should be able to solve this by using the "Advanced" button for the water drawing tool, unchecking the "Restrict to map border" box and then save the tool. Then redraw your river, making sure you draw the ends a little way beyond the top and bottom map edges. DO NOT use the "C" = "Corner" option, just add a few nodes and make the ends of the river outside the map border a bit more rounded, with fewer nodes close together. The screen should hide this once you're done (or if not you can use the COLLAR commands to create a new, larger one - use COLLARDEL first to remove the existing screen, and then COLLARAUTO to add a new one - if I've remembered that right).

Hopefully, that'll cure this point at least. Good luck!

This blog posting by Remy Monsen might be worth reviewing, as it will allow you to create an image of whatever you wish that looks as if it's been cut into the surface involved.

Looks good.

Obviously, the Empire of the Sun Annual would work nicely for a map of this kind, based on your sketched style, but that wouldn't provide nearly so many building/structure options. For clouds, you might try the cloud symbols in the Alyssa Faden Annual. I'm not sure there are other separate cloud symbol options, although SS6 does have some chimney smoke plumes (they look a bit too smoke-plume specific to be ordinary clouds, however, unsurprisingly!).

Might be worth thinking of moving the mountains further back overall, as they don't look quite right where they are now; too sharp and clear. Maybe add a misty vale in between the building and mountains/trees, and/or just add some mist (transparent irregular polygons of white/pale grey) to fade them a little, and give the impression they're more distant.

Ctrl + F should do it, I think. It's the same command as Tools -> Drawing Aids -> Toggle frames using the drop-down menus, because what you're doing is toggling the frame (thin white line) options to show where the nodes are on a line.

Thinking about the late-stream discussion regarding using the "normal" Mike Schley city symbols to create a top-down map, and then the isometric ones to show a pictorial impression of the place on the same map, with Ralf's comment about using vignettes to highlight important individual places within the settlement similarly, brought to mind the Middle Earth poster map prepared by Pauline Baynes (Tolkien's only approved artist during his lifetime). Digging around online, I've come up with this reasonably high-res version of the original on the Museoteca website, which shows why it came to mind. I used to have a copy of the poster, sadly lost somewhere along the decades since, though it remains strong in my memory!