I felt the same way for a long time. It took several months after I started really looking seriously into transition before I was able to feel completely comfortable and certain that it was the right thing to do. And you know, sometimes I still find myself feeling a little bit "she". But for me, having the male body presentation was much more important to me. (I see myself as roughly 85% male, 15% female.)
Like others have said, a good gender therapist can help you sort through your feelings on the matter. On the other hand, be aware that some of them are prone to filtering their clients experiences through their own, so they may unconsciously push you in one direction or the other. I know my therapist was all set to write me a T letter before I was really ready. Fortunately I had some well-timed financial setbacks that made me put on the brakes for a few months.
