Thus was born The Trials of the Youngest Princess, and a couple short stories. The story is of a princess, the oddball in the family. As a daughter, she was lacking in some knowledge a son would long since been fully versed in, but I simply had to make her a tomboy, and a tomboy before there ever was such a thing was rather fun to play with. Allowing her to do something I've always wished I could do, I allowed her to learn how to handle a sword, but as a daughter, this could never be known. As a tomboy, she was constantly searching for some way to feed this passion. One day, when she discovers her father and brothers had been murdered, and who knows what had happened to her mother or her brothers' wives and children, she has to run; she has to preserve her life as possibly the last living member of her family. And she has to find some way to exact revenge.
The story could have hosted either gender, but many key points would have been very different if a boy had been the main character. At the very least, expectations, both by and of, the main character would have been very different. Since my young woman began her desperate journey at the age of seventeen, she very much needed the protection and experience of the swordmaster, the only person who knew of her skill with the sword. A boy, however, in this environment would have been learning the sword since he was about six and not in secret. Excursions into town might have been with his brothers at first, but not necessarily - maybe at first, say up to the age of twelve. A boy would not have needed to develop a disguise in order to participate in any of the events he wanted to, in fact, he may well have been encouraged to do so.
Differences in men and women are many and varied, but mostly if comes down to the logical choices they make, and the logical expectations of those around them. Other differences I probably don't need to mention but I'll list a few, as they are important to consider.
Emotions is one - most women are emotional to some degree. Tears will flow, and sometimes at inconvenient moments. Most men will try, usually successfully, not to cry. That's not to say it doesn't happen, but the event has to be rather intense, and possibly solitary, as in he's alone.
Body-language is another one - hands are a big key to communication, but men and women use them differently. Women are very open with their hands, waving them openly as if to brush their ideas into the mind of whoever they're talking to. Men use them as if to reinforce their stance with clenched fists or crossed arms, or even shoving them in their pockets. Head, shoulders, and hips is another drastic difference in body-language. Women will flip hair back - men will shove it back or rake it back. Women will, consciously or not, angle her shoulders in direct proportion to how she wants men to perceive her sexuality. Men will do much the same thing, but for a different reason. Yes, he's trying to impress her or trying to shoulder the responsibility of the world. Hips, well most men just don't have a lot of flexibility there whereas women habitually sway as they walk. Now, this last thing is dictated by environment. Sway your hips while walking through rough terrain and you'll throw your back out, so the swaying of the hips is a learned move - keep that in mind.
In Huckleberry Finn (I think) it was body language that gave Huck away. He was dressed as a girl, but he wasn't getting it quite right so a woman tossed something to him and he clapped his knees together to help catch it. She pointed out that a girl would have done the opposite allowing her to make use of her skirt to help with the catching. I never quite saw it as true, but then at that time, with girls wearing only dresses, I suppose it would be a logical development. Boys, better at catching with their hands, would not have relied on a wider field to catch a tossed object.
So it's these small details that make all the difference. Make your guys be guys or make your gals be gals, whatever their age.
Like my friend did for me, I now pass it along. If you only write with women as your main character, I challenge you to write your next story around a guy, and if you only write guys as your main character, switch it up and put a woman in there. You can do it. It's not as hard as it sounds, and you don't really have to change your story elements all that much.