The full backup of the Video-Enabled 3DS is done. Holy cow that was a lot of work, but (1) everything is now backed up to it so I can stream pretty much anything off it and (2) all the save data is transferred, so it's just the way it was when I last used it (including all the finished Zelda games, and Super Princess PEach).
Rook all day, but it's done. Most of the hard work is over, though, so I'm thinking the NN3DSXL with the wonky Game Card port won't take nearly as long.