Sorry I'm not bringing an answer. Only a small idea with the grey box: is it that fairy is not a type in gen 5 so the essentials folder doesn't contain a pink picture to show it's a fairy type move, probably just need to add a "fairy" called picture in a certain folder where the others are.
For the sprites I never touched the script about them, my suggestion would to open the battler picture of fennekin and compare it with a gen 1 one. Is the picture the same size? is the pokemon placed in the center in both pictures? In general if you're not comfortable with script (which is still my case) then it's easier to change the pictures