I had doubts ALL through transition.
Pre-transition, I was actually only starting hormones as a "test," to see if they were really what I needed. I was afraid of admitting to myself that I DEEPLY wanted them. For the next 5-7 months, I was constantly fighting the voices in my head which were so damned scared that I couldn't do it, or that I was going to have regrets, that it would never work, that I'm not REALLY female, that it's just going to be a phase, that I might get sick of it and change my mind, that I really did seriously question myself. The first times I ventured out in "girl mode" I was seriously like "OMG, is this seriously what I want for the rest of my f***ing life? I don't feel like a girl, I just feel like a freaking drag queen."
When I was fired from my job the first time, I seriously took time to step back and ask myself if I really knew what the hell I was doing. Were these mood swings ever going to settle down? How the hell was I ever really going to be able to get over my insecurities and EVER go full-time and be comfortable with it if doing something as simple as wearing clear nail polish on my fingers to work turned me into a nervous wreck? Around the 1-year-mark I started worrying that it was hopeless that I'd ever pass, that I was just going to be some he-she-it freak if I continued transition, because I'd NEVER been gendered female, even despite 11 months of hormones and growing my hair out and switching to an androgynous wardrobe.
Even after I finally did start getting gendered female, I still had doubts that I could transition... I was terrified by whether I'd be accepted, whether women would really be okay with calling me one of their own, with being able to use their bathroom, etc, etc. After getting fired from yet ANOTHER job, I seriously started being afraid that transition was just going to destroy my life, and that I might have no choice but to abandon it and go back to being male to keep my working life afloat at all. I had a REALLY hard time making the mental jump from "I wish I was a girl, I want to become one," to "I AM a girl." That step was really hard, and made me have some doubts right after going full-time.
And even post-transition and with a stable job again, I'm still sometimes doubting that I have the mental strength to keep doing it, because I'm still fighting dysphoria about how I still don't look like the cis girls look to my own eyes. And I have some really bad self-critical bouts where my mind is like "I'll never be a REAL girl, so why even bother?"
The thing that kept me going was knowing that I really did want to be female... what I was doubting wasn't my own gender identity, they were just fears and feelings of inadequacy and the complications of being a trans woman in real life getting to me. And so I pressed on, and fought through all of the fears and doubts, and now I am indeed finally relaxing and getting a bit more comfortable with myself. I still have occasional doubts, but they usually only show up during dysphoric bouts. The rest of the time, I'm just living my life, being myself, and not really thinking about it anymore.