I recently came across an article published by a Univeristy that explains this--I'm so sorry I don't have a link to it, if I find one I will post it here!
Anyway, although it sucks, when it comes to health insurance you have to sign up as the gender that is expected to have the treatments you will need. If that makes sense! Basically, if you have female parts but are male, for the sake of remaining a healthy human you should register as a female. Insurance companies will not cover medical expenses for female only procedures if you are registered with them as a male. What you could do is put female and then at some point try explaining to someone what you meant. To further complicate matters, if you have had your name legally changed, and your gender marker changed, you may run into some problems. But you should be able to get it all resolved, its just going to take a couple hours on the phone and pry some doctor's letters!
There is also the possiblity an insuranced company could refuse you, so be prepared for that.