You'll need to unblock the zip file before extracting it as described in nthe start of
Yeah, you'll have to remove the ability first. This cutscene is a little brittle.
Looks like one of the important files is missing. Depending on what changes you made, it may be easiest to start over, making sure to save the project every chance you get.
I'm afraid not. Its save file structure is rather complicated and requires having complete knowledge of how it's structured to edit things effectively.
I recommend using Layered FS to not need to install anything else. nxdumptool can dump ROM files straight to the correct directory, and Sky Editor DX is designed to use this.