Figuring out your sense of identity can be a real struggle. I'm still working on it myself, and I still have bad days, but I'm making progress overall.
We're surrounded by a society that has all sorts of expectations for how women are, and not meeting enough of those physically or in learned social skills has a way of bringing up doubts. I'm not 100% feminine 100% of the time, which is true of many women; I could also be non-binary, but trying to focus too much on my internal sense of self and what gender I really am was stressing me out and driving me nuts!
I went into HRT expecting that over time I would feel distinctly more female, as my sense of my gender was vague and sometimes varying before that. Instead, what's happened is that I feel like myself, and I didn't really know what that felt like before. In my case the only automatic sense of gender that feeling like myself comes with is that male isn't right, and everything else I just have to figure out over time.
In order to avoid obsessing over my internal sense of identity and constantly stressing myself out over it, I asked myself some questions. Be careful as a few of these at least partially rely on being able to put society's expectations on hold for a bit or being out and accepted by a few people:
Do I feel better on HRT mentally?
Do I feel good about the physical changes HRT brings?
If I ignore the mirror entirely and think only about how I feel, does wearing women's clothing feel better, or worse?
Does coming out and being accepted make me feel better, or scare me away from transitioning?
When socializing, do I feel more comfortable with women or men?
Do I feel better when others treat me as a man, or a woman, or neither?
What pronouns *feel* best on average? Not which ones feel most automatic (patterns are hard to break), but what feels good?
When I process things mentally and emotionally, does it seem to be a closer match to the way cis women process things, or cis men, or neither?
In my case, I finally just said, if I want to look like a woman, and have a body like a woman, and I feel more comfortable interacting with other women who are treating me like a woman, and I usually feel better being addressed by female pronouns (even if I don't always make the connection yet that they're referring to me), and I seem to process things mentally and emotionally like the other women around me, and I feel better in women's clothing, then I must be a woman, and my occasional thoughts of being male or neither are just due to years of being told otherwise and internalizing that. Old patterns are hard to break, even if they're actively making your life worse!
I started having a lot of doubts around 3 months into HRT myself, but I felt better after another month of transition progress. I wrote about that in this thread (forgive the name change - I'm still struggling with that part!):
https://www.susans.org/forums/index.php/topic,239870.msg2161532.html#msg2161532I hope you can start feeling more comfortable with your own identity as well!
-Lisa