I've recently been pondering this in terms of anima/animus. In the strict Jungian sense, men have anima (the female archetype) as their inner voice, women have animus (the male archetype). But for those of us who are trans, does that get reversed or are we stuck with the archetype from our biological sense?
I personally believe that soul/spirit/whatever is genderless and that our bodies are fluid. If an MTF (sorry, FTMs, been pondering this from my own point of view) was born with a biologically female brain and a male body, and always self-identifies as the opposite gender from their biological sex, then that person is, for all intents and purposes, female. It would then make sense that animus is the guide for the MTF as anima would be for the FTM (though for different biological reasons, obviously).
The only time I can remember feeling a powerful, definitive anima presence was in a pair of dreams back when I was 13. I dreamed that I was getting married, but at the last second, she said she had to go and left. The next day, I was so devastated by my dream image that I couldn't stop crying. I wished desperately for her to come back so we could be together. That next night, I got what I wished for. She came back, apologized, and explained that she had just died... though the plan was for us to be together in this life, it was no longer possible. That's the last time I ever saw her, but I've never forgotten. I've suffered gender dysphoria since I was at least 4 (the first time I remember shunning the company of other boys and praying to wake up a girl the next morning), so that dream, right on the brink of puberty, was striking in its timing, clarity, and message.
Was she the anima who would have guided me as a cisgender male? I've finally, 20 years later, come to terms with my transsexuality and began hormones and RLE. Did animus not show up these 20 years past because of the void in which I lived? Is this why I turned into a hermit and preferred to drown out my inner dialog? I don't know, but I keep hoping that some night soon, I'll see something that gives me the answers I seek.