Don't worry about manual focus, leave it on autofocus. It won't affect your aperture. Having a look through your shots they look better, all but the last one looks a little underexposed to me. But definatley better. I do notice these are all at ISO 1600, is there a reason why you kept it at that setting? It's great if you are not getting movement blur at 125th though! More depth of field would be another improvement that could be made (as others have pointed out by changing your aperture to f8) though looking at your settings this would mean that for the same exposure your ISO would be maxed out at 6400. Which is not necessarily an issue but it is an indicator that you may need supplimental lighting for the group shots of the ferrets.