It doesn't matter a bit that she's not an official gender therapist. That's what you were seeing her for, and you were living as male during the time you were seeing her, so it's entirely natural to ask her. Since you haven't seen her in a while, she may want to do a "checking in" session or two by phone first; you'll probably get maturity points if you suggest this yourself.
As long as she's a licensed psychologist or other legit mental health professional, there should be no problem having her letter accepted.
And it would be fine to call her, I think. She's a professional and will be used to being contacted by former clients -- it happens all the time. Not all MH professionals do email, because there are major privacy/confidentiality issues with that form of communication.