Kevin, I replied to your PM but completely ignored your question re: cropping, so I'll answer it here. Sorry about that!
Don't be afraid to crop. If you are shooting live subjects and you don't have anything to brace yourself with, then it can be difficult to maintain focus and position of your subject in frame. As a result it may be better (or you'll get a better hit rate) if you leave some space around the subject and crop later.
With a 1:1 macro lens, you may still not be able to fill the frame with your subject, so you will have to crop a bit regardless to get the image you are after. As I said, I am not familiar with your lens, but this may be the average for a 1:1 lens, but I think you may be able to get a bit closer. I doubt switching to manual will help much in this regard, however, although I would still recommend switching to manual if only to improve your focus technique.
I use canon's MP-E macro lens which is unique in the market for offering a 1-5X magnification (sadly there is no nikon equivalent) but this allows me to change the magnification to suit the size of subject I am shooting and fill the frame a bit more if needed. You can achieve the same thing with bellows or extension tubes, but this is usually more of a faff, and you have to estimate the required magnification before approaching your subject.
As for general critique I agree with snagsanger. It looks like your DoF is too shallow, so hardly anything is in focus. That said you state you shot these at F11, which is similar to what I would go with at this magnification (I usually shoot at F13 at 1:1). Looking again at the first two posts it seems to be the edge of the wing that is the focal point, so is a bit in front of where it needs to be; always the eye! This could easily be the autofocus getting it wrong so again, another reason to switch to manual.
EDIT: I've just looked at the uncropped images full size and indeed your focus point is too far forward. Look at the texture on the paper to see where it is and you can see it extends in front of the fly's body rather than over it. Switch to manual then slighty rock yourself forwards and backwards to control the focus point. Practice a lot and good luck!