To start, I completely recognize myself in what you say about the Church having been a major healing power in your life; I would not have been alive today if it was not for Her. She literally saved me; when I converted, I had major self-destructive tendencies, which would have killed me if not for the Church. I managed to go back to college and complete my first (but useless, so I've now started over with something less lofty) degree because of Her. That said, my problems were ultimately from being trans, but entering the Church kept me alive for long enough to come to that realization and stop repressing myself.
Realistically, you will have to give up being a lector - there is no discipline to bar trans people from functioning as one, but since it might create controversy, I think most priests would tell you to step down. And that is their right; a priest cannot be forced to accept any person as lector or altar server, even by a bishop. A priest also has the right to refuse having lay lectors at all - it is a possibility, not a requirement. Personally, I stepped down from being an altar server, which I truly loved, especially in the Extraordinary Form (I simply love smashing stereotypes by being a transgender liturgical traditionalist, by the way
). I miss it, but I do not miss pretending to be a man, so the choice is simple.
Additionally, it is a fact that the Church generally reacts negatively to pressure, and the biggest changes tend to happen when there is little pressure. For this reason, I'm against activism directed at the Church - it is generally counterproductive, and I am a pragmatist. The fact that you are okay with stepping down and simply being in the pews, will make things a lot easier for you, whether it is right or not.
This said, you have
every right to go to Mass, to receive Holy Communion, and to go to Confession. Transitioning does not in any way bar you from these sacraments. I've written a more comprehensive summary of Catholic discipline and teaching related to trans people here:
https://www.susans.org/forums/index.php/topic,171318.msg1497122.html#msg1497122Personally, I have however ended up mostly not going to Mass until I can blend in again - at the time, I present obviously trans, and I can't bring myself to go in guy mode anymore. I also don't want the attention I know I'd get from some individuals if I went in my current state. I miss going, and I don't like not fulfilling my Mass obligation, but I also have to acknowledge that at this time, my absence is health related, which does reduce or remove culpability related to missing the obligation. I do however look forward to being able to go again, without attracting attention. At the same time, I suspect people wouldn't react as negatively as I fear if I went now, but at this time, such anxiety doesn't do me any good, rooted in reality or not.
However, that is my personal choice, and not one that I would even recommend. As long as you don't dress provocatively,
people have no right to complain. I would even say it would be un-Catholic of them to do so. You have
every right to receive Communion and go to Confession. Your treatment is a medical necessity, and hence
not sinful. Those who might disagree (including priests and even bishops) simply don't understand the nature of being transgender, and the nature of the treatment. Many also don't understand Catholic teaching about gender and medical treatment.
To conclude, don't stop going altogether. You have a place in the Church. We all have. If it gets tough, speak with your priest. As a last resort, switching parishes might make things easier; I consider starting to go to a Dominican church (not a parish, but they function as one socially) in my city, where I might be less visible. I know several of the priests there, but few others. At my current parish, i stand out simply by not being an immigrant, and my current presentation would make me stand out even more. The immigrants are also considerably more conservative. At the same time, ethnic diversity is what I love about my parish and why I chose it in the first place, so it is a difficult choice!
Lastly, you should know that those of my Catholic friends I have come out to this far (and I would describe them all as orthodox), have all been overwhelmingly supportive. They fully realize that I'm doing this for good reasons, and many of them had already figured out that I was different in some way. I know some of my more remote acquaintances might react differently, but at least this shows that many (I'd say most) real-life Catholics are sensible people who are fully aware that life doesn't always fit in neat categories. The real Church is so different from the "online Church" - it saddens me that most non-Catholics are primarily exposed to the latter.
Edit: I should also mention that while yes, the teaching authority of the Church, expressed through a Council or the Pope on his own under very specific circumstances, are seen as infallible,
but only when they solemnly proclaim a dogma in the domain of faith and morals. This happens extremely rarely. There is certainly no infallible teaching about the determination of gender, and there can't be, since it is a matter of science. Gender is determined by doctors, not theologians. There is neither any infallible doctrine on the morality of transgender medical treatment. The post I linked has more details about this.
