Thank you all for the positive comments, that makes me feel a lot better about what I've written.

Rowenna, I'm so glad you posted your letter! Your mentioning God made me realize that is something I definitely need to address. I believe, but am quite a bit flexible when it comes to the nature of my belief as I identify as simply a Deist, and sometimes forget that my father is more traditional despite his lack of church attendance. I think taking time to address the issue in context may help him with acceptance. (Mirroring what you said, that God could not have intended this middle ground. Instead, perhaps it being something that I was meant to overcome and work through.)
Colleen, trust me I could have gone on for another 10,000 words.

I had to stop myself before I spent all day just typing, as I had that same realization that information overload probably isn't the way to go. (Particularly since I do actually have some school work to be typing as well.

)
Since my father is a psychiatrist I definitely am taking a "here are the symptoms, the diagnosis can't be denied" approach. Unfortunately, despite being a reportedly great psychiatrist, when it comes to family he is a master of ignoring what he doesn't want to see(hey, just like I was!), so I sort of felt that I had to pose it in a way that left no room for doubt.
I don't know when I will work up the nerve to actually give this to him or talk to him, but I know that I hate this feeling that I'm living a secret life, that I have to hide everything. (Not to mention panic involved as packages of women's clothing and makeup trickle in, wondering if this will be the one someone else accidentally opens.) I'm just not cut out for subterfuge (well, with anyone but myself anyway I suppose.)
Also, rereading it again with an hour or two removed I realized I need to rewrite some of it simply because some of what I wrote may be construed as being negative/insulting towards those of us who do wind up in hospitals and psych wards over trans related issues. It definitely wasn't my intention, but now I feel really bad reading what I wrote because it seems like I was saying "I'm not one of those crazy people!" or something like that, out of my fear of what his expectations may be.
(Edit: Addressed what I just mentioned in the original post with an edit there too.)