when I have some time, I'll ask manta2g for the java snippet which helps in menu control. It's very likely a simple adjustment which could make it so it's at least not quite so sensitive.
Sure, although you could easily do it yourself, by reselecting the category after selecting to edit the story, which will bring up the menus for the sub sub categories.
The pair specific categories were not removed, they were made sub categories of the pair types they belonged IN. It helps to make it so that the query load is less, which is better for the database.