At one point I had symptoms somewhat similar to the ones you describe, Zquence. I was diagnosed with two different dissociative disorders at different times. In my case, I got that way because of severe childhood abuse. I chose to deal with only the abuse issues for many years. I thought that when I finally got well, the gender identity stuff would go away. In reality, it got worse. I now wish that I had spent at least some energy working on the gender dysphoria while I worked out the abuse stuff.
I can't say whether it would be a good idea for you to transition at this point--you may need to get a better sense of your internal system as a whole before you make any permanent changes. It might be good to consider yourself genderfluid for now, and dress and present yourself in whatever way feels best on any given day.
I'm really glad to hear that you have a therapist. Don't be afraid of psyche professionals. They work for you. If one is treating you badly, or if they just aren't helping, go and find another one. A good therapist can make all the difference.