In the days of Shakespeare, girls/women did not tend to act. Considering that the actors were probably all male, what special challenged did Shakespeare have with producing this play in a manner where the audience would not be confused?

Of course there is comedy to be mined by dressing up males as females. Still, he had to make things believable. Shakespeare often used pre-pubescent boys in "female roles". As well more elaborate costumes/wigs might have been used for the gender disguise. Voices were altered to reflect gender as well. Audiences were also well practiced in imagining certain scenarios that were difficult to stage.