consider getting yourself a .22, it will be cheaper and easier to practice in.
The .40 has a pretty stout recoil for a new shooter and something like a flinch takes a lot less time to form than it does to get rid of. It would be a good thing to teach your wife with.
That being said, you are a lot like myself as far as your hands and eyes are concerned. Right handed, left eye dominant. It makes me prefer my left hand for shooting anything, you will probably find that you are the same.
As far as your wife's eye problem, this might take some special consideration for her to shoot accurately. Consider a decent red dot sight or laser on a home defense option in the long run. I think a red dot might work for her because even when the perspective of your eyes and the dot shift, the bullet goes where the dot is, the same idea applies to a laser. Is the spot in her vision in one eye or both?