I ended up mapping the Valley area. It's not all that interesting looking, but it's done at least. But for any other cut scene that's no more than one screen in size, I'm putting my foot down and not doing them. If anyone wants to see them so badly, they certainly can when they play the game.
@vorpal86: Thanks very much! By the way, what are you refering to when you say "The cut-scenes for the Boco run"?
Also I'll mention that for the last dungeon, I decided to split it up into seven maps, one for each distinct area (desert, ruins, forest, cave, tower, castle, last floor). The Town of Mirage won't be included in those maps since it already has a map of its own. I found that it was a bit too cumbersome having everything in one huge map, and I don't think it'd be all that useful to people who actually want to use it as a reference for where items are located and whatnot.
Now that I think about it though, I may as well make one huge map as well, for those who want to see everything in one single image.