If you wanted to go totally nuts, you could dremel the edges just a bit and then sand them gently with about 500 grit, test fit them, and then paint them once you're satisfied. You may notice that the fitment is currently a bit tighter at the bottom that at the top. This may help to alleviate that. A lot of work, admittedly, for a part that makes the car run no better at all.
I might also suggest the "percussive maintenance" approach, wherein you perfect the art of beating the crap out of it from the bottom with the heel of your hand until it fits satisfactorily.
If you're a real perfectionist, have your body guy bondo right over them, sand, and paint, leaving no evidence of a gap, creating a one piece look. If you do this, you'll have to make sure that you have a way of making sure that the skirt stays suspended properly, as, from memory, there's a body pin up under the jack cover holding the affair to the car, and you wont be able to get back in there after you seal up the jack point.
Or, find a spot where you can't see the jack covers at all, like the front or back of the car, sit down on the lawn, crack a beer, light up a cigarette, and forget about it.
