Here's a tough question I got from a reader the other day. I'll do my best to answer it, but I bet it'd be even more useful if others weighed in, too.
Can you do a post about how you know you're female even if you're gender non-conforming at some point in the future? I feel like an alien in a Halloween costume when wearing women's clothes, even if they're not overly feminine. I don't feel like a dude, but I don't feel like a woman either, as far as I can tell, but if you aren't into being girly, how do you know if you're a woman? My best friends are straight and I don't know how to talk to them about how they know they're women. I wear all men's clothes, and I really like getting called sir, but I think that's only because I get called miss maybe 70% of the time, and sir 30% of the time, and I like knowing I'm ambiguous.
First: good for you to have the courage to ask these kinds of hard questions about yourself! That's awesome. Second: I'll give you the best answer I can, but I can only speak from my own experience; you should definitely talk to as many people as you can.
I had a conversation with my buddy C about something similar yesterday. We were talking about gendered pronouns (we both use female pronouns, but are often called "sir" and don't mind it), and I mentioned that if I was a kid today (I'm in my 30s), growing up in a progressive area of the country (which I didn't), I wondered if I'd have identified as trans. Why? Because I totally didn't fit in with the other girls. I didn't outgrow the "tomboy" thing--in fact, it became more pronounced as I got older. I wished desperately that I could wear a tux to prom instead of a dress (ugh). I can remember once in third grade, actually praying that God would come and turn me into a boy. I felt much more at home with boys than girls. Girls seemed foreign and hard to understand. Boys made sense, and played cool sports. (Mind you, I didn't feel like I was a boy, which many trans men report having felt.)
For me, identifying a boy would have solved this particular conflict. But at the same time, I didn't feel uncomfortable in my own body (unless it was wearing women's clothes! I was like you, in that I preferred men's clothes even to non-girly women's clothes). It wasn't my body that was the problem--it was the culture around me (and the gender-based expectations and assumptions that culture contained) that were the problem. I thought my breasts were kind of inconvenient, but I never felt like they weren't "mine." As far as I can tell, this is a big difference between butches and trans men. (You might be interested in this post about why female-identified butches are different from trans men.) It wasn't until I started to meet butches and masculine women that I realized, "Oh! That's what I am!"
Some days it would be nice not to get stared at in public, which I wouldn't if I was a man in the same haircut and clothing. But I don't feel like I "am" a man. I don't want to use the guys' bathroom. I like getting called "sir," as long as it doesn't happen all the time. It reminds me I'm different. Being a masculine woman just feels right to me. I don't feel alienated from my lady bits--especially not when they're under a shirt and tie. But put women's clothes on me and I'm suddenly an alien in my body. This tells me that it's clothes and culture that are the problem, not my gender identity. For my trans male friends, they didn't feel comfortable in their bodies no matter who they were with or what they were wearing. Even if they were alone in the shower, they felt as if they were in the wrong body. They hated being called "she" or ma'am. (I'm not saying this is the experience of all trans men, just of the ones with whom I've talked about this.)
Until I was in my late 20s, all my best female friends were straight, and often fairly girly. Even when I was married to a man (that's a whole other story--here's a link to part 1 of that five-part story if you feel like reading it), I didn't feel like I fit in with the straight women. Now that I'm an out, proud, lesbian masculine butch woman, I feel like my straight female friends know I'm different from them, and respect it. I don't think they see me as less of a woman, just as a totally different kind of woman. And they often treat me more like a gay male buddy than like "one of the gals." This took some getting used to, but I actually like it now. The key point? Just because you don't conform to society's ideas (or straight people's ideas) of what "being a woman" means, doesn't mean you aren't a woman!
I should also point out that a lot of people don't identify as male or female. Some identify as neither. Others identify as both. Some women get top surgery, because although they identify as women, they don't like having breasts. Some trans men keep their breasts, because they like them or their partner likes them or they can't afford surgery. There are all kinds of possible gender identifications and expressions. Although boxes like "male," "female," "butch," "trans man," "genderqueer," and so on work for lots of people, that doesn't mean they have to work for you. You can also pick more than one. You can also change whenever you want. There are no rules about gender, only patterns. You don't have to follow one that's already been laid out.
I'm glad God didn't answer my third-grade prayer to be transformed into a boy. I love being a butch woman. There are hard things about it, yes, but overall, it just works for me. Keep questioning, experimenting, and looking for answers about your own identity, and I bet it'll become clear what works for you, too.