I don't know whether this is of any help to you at all, but many of us MTF and transfeminine people in the over 40s age group were prenatally exposed to a powerful artificial estrogen called diethylstilbestrol (or DES), that doctors used to give to pregnant women as a treatment for preventing miscarriages. While the DES exposed daughters are acknowledged to have all sorts of problems with cancer, infertility, abnormalities of their internal reproductive organs, autoimmune disorders and so forth, the official line is that the male babies from DES pregnancies suffered virtually no ill effects as a result of their exposure. In reality, for many of us, it appears to have caused our process of sexual development to go spectacularly wrong, with our brain development tending to have borne the brunt of the effects (although it seems to have given many of us a subtle feminine cast to our appearance as well, and among the people I've talked to, physical intersex-related genital abnormalities seem to be quite common too, such as hypospadias, cryptorchidism and micropenis). As far as brain development is concerned, in my case it's very much an intersex condition, but most of my DES exposed facebook friends seem to have undergone overwhelmingly female brain development and are MTF transgender. This may be what happened to your father, particularly if his mother had miscarried prior to falling pregnant with him, or was in an at risk group such as being very young or aged over 40.
In any case, irrespective of what caused it, being transgender is the result of inappropriate levels of androgenic hormones being present during the critical period in fetal development when sex differences in the brain arise - insufficient androgens in the case of MTFs, too much in the case of FTMs. There's a popular misconception that X and Y chromosomes determine your sex. In fact, all being XX or XY does is determine whether you develop ovaries or testicles, everything from that point onwards is hormones. All it needs for a person to become transgender is for them to have the appropriate hormones for their genetic sex during the first trimester (which is when all your physical sexual characteristics develop), but for something to go wrong with their hormones subsequently.
For the first 16 weeks of brain development, there's a process of very rapid cell division going on (to make up the enormous numbers of cells needed for the human brain), and migration of those cells to where their final place in the brain will be (which is often far from where they form). So, although there is a brain there, during those first 16 weeks the whole thing is in a state of flux and is being continuously rebuilt. That probably explains why androgen levels during those first 16 weeks don't seem to have much (if any) influence on the eventual sex of your brain.
By about week 16, the first cells have reached their final position in the brain, and start growing their permanent connections to the other brain cells they're going to be connected to. This is a process that continues at a high rate for the remainder of the pregnancy, and is presumably one of the ways in which the differences between male and female brains arise. I'm guessing that there's a "male way" and a "female way" of wiring up brain tissue which are subtly different at the cellular level.
Another thing that happens during the later stages of the prenatal period is a process of programmed cell death, in which excess brain cells are removed. I went through an exercise of trying to figure out all the ways I'm different from ordinary men, and one thing I've noticed is how they get all excited and their faces light up when they're watching competitive sports. Try as I might, I've never been able to experience whatever it is that they're experiencing. To me, it's just a pointless activity that I can't muster enthusiasm for. I'm speculating that there's a critical period during which the brain cells that drive aggressiveness and competitiveness need there to be high levels of testosterone there, otherwise they'll undergo programmed cell death. In my case the testosterone wasn't there at the crucial time, so those cells didn't survive, and now the only way I can act aggressively and competitively is by creating some fake behaviour to do it.
One thing I realised is that an awful lot of the person I was, was actually fake, and something I'd subconsciously constructed when I was young, by observing people and imitating their behaviour. Reading other people's stories, this is something that seems to happen a lot, certainly among those of us in the older generation anyway. People in general and adolescents in particular often react very badly to female body language and feminine behaviour coming from someone they perceive as male. As a child it didn't matter so much and I was able to make friends and play with the other kids. The moment I hit puberty though, that all changed. My childhood friends all abandoned me, no one wanted to know me or be associated with me, and I was bullied mercilessly for "being gay". On top of that, I think at a subconscious level I was expecting to go through a female puberty, and it only added to my distress when I started growing facial hair instead of breasts. It's the only time in my life I've ever seriously contemplated suicide. Your father probably went through something quite similar, I've seen plenty of other stories where similar things happened.
As I got older, I learned to modify my mannerisms and behaviour to make myself more passable as a man. In due course, my life became a fairly unremarkable existence working in the computer industry. I never felt settled though, and always had a feeling of sadness permeating through me without any indication as to what was causing it.
Then, in 2010, I suddenly had the thought that my instinctive social behaviour, as well as the way I experience arousal and orgasm, are a lot more like what usually happens in a woman rather than a man. That gave me the idea that perhaps some of my brain development had somehow occurred as female instead of male.
One effect of being socially excluded at school was that it made me turn away from the world of people, and put all the energy that would normally have gone into building and maintaining social relationships, into instead trying to understand how the natural world works. I became one of the top pupils in my school at sciences, and excelled in chemistry and biology in particular. My obvious career choice would have been to go into medicine, except I wasn't having a very happy time, and it affected my studies enough that I just missed out on entry into medical school. Although I ended up working in IT instead, I've retained a kind of amateur interest in the sciences ever since, which meant that I was in a better position than most people to try to figure out whether, firstly, it's even possible to have a brain that's partly developed as male and partly as female, and if so, what might have caused it.
The short answer is, yes it is possible, and one of the things that can cause it is exposure to external hormones during prenatal development. This is something that's been shown in a wide range of animal species, including mice, rats, sheep and monkeys. Although both parents are dead and I've no way of knowing for sure what happened while my mother was pregnant with me, the physical symptoms I have (including a type of body structure called "eunuchoid habitus", which is normally associated with intersex conditions), as well as the social difficulties I experienced as a teenager, all seem to match what happens with DES very well. The main difference is that, in my case, it's only gone partway through, so I've ended up with a gender identity that is more like a mixture of man and women, whereas DES miscarriage treatment seems to more generally produce people with a gender identity that's overwhelmingly female.
DES was used in millions of pregnancies throughout North America, Europe and Australasia, so there must be a lot more people out there like me, my facebook friends, the people who've posted about DES on this site, and the other AMAB people I've talked to online over the last few years who were prenatally exposed to DES. I, along with a number of other people, have been trying to get the story into the news, without much success so far unfortunately. I guess it sounds too outlandish for most reporters to even give it a second glance. Some of us did get a story about DES on a Florida based TV station (WTSP) last year, but unfortunately other media outlets haven't picked up on it so far.
Anyway, as regards your father, unfortunately there's no way of changing what's there. The animal research shows that there's a critical period early in life during which hormones influence the sex of the brain. Once that critical period has ended, that's it, whatever's there is now permanent, and stays with that animal (or person) for the remainder of their life. Decades of clinical experience confirms that what applies to animals applies to human beings too: your gender identity is already set in stone by the time you're born, and neither hormones, reparative therapy, ECT nor anything else can subsequently change it. It's true we can do a much better job of faking it than most animals can, but at the expense of making ourselves chronically unhappy and unfulfilled.
