The reason the drawing tools all seem to use the same fill is because they are looking for a fill that does not exist in the current map, so they fall back to the currently selected fill instead. This is an indication that your style isn't set correctly, since each style typically have it's own fills.

To get the tools showing the proper fills (for the style they belong to), you can import the fills into your map using the procedure described here (but I do suspect that isn't really what you need here, you probably wish to use the correct tools, not the correct fills from the wrong tools.):

Looks like your dungeon menu file isn't properly up to date. I have that option with the Naomi dungeons. Try running the latest update again (In any case, the command isn't restricted per style, you can always just switch to another menu temporarily.)

As for your map, your MAP BORDER layer is spammed with entities. All those green, purple, and orange shapes are on that layer. They're the ones messing up the restrict operation.

To elaborate why you get that "Clipboard empty" message.

CC3+ doesn't embed images in the drawing, but link to external files. This is why you can't simply paste from the clipboard, since the clipboard isn't a file CC3+ can refer to.

The reason it is reported as empty however, is that the Windows clipboard is kind of smart. It can keep the same data in multiple formats (for example, if you copy some text from a web page, the clipboard will store both a plain text version of the text, as well as a formatted version). Whenever you paste, the clipboard will pick the version that is suitable for the program you try to paste into. However, the only thing CC3+ can accept are either plain text, or CC3+ entities, and after copying an image from somewhere else, the clipboard won't contain any of those. Therefore it is empty as far as CC3+ sees, because it doesn't have anything to offer that program.

Are those lines 0-width lines? Try making them a bit wider, thin lines can disappear when output to an image, which again would prevent them from having any effect.

Originally, the dialog had you input numbers from 0 to 8, but people found that confusing so the scale in the dialog was changed to a more familiar 0-100 scale, but the effect still uses the original scale internally.