Doubted myself on and off, eventually came out to myself as trans. Then doubted myself some more. At some point, I was pushed to the point that I came out to my parents, possibility of negative reaction be damned. And since then, I have continued to examine myself and I am more sure than ever before. When I came out, I started by identifying FTM. It didn't change and I still identify as male.
Yes, everybody doubts (or, really, if they don't they really should) doubting phases force you to be honest with yourself and (hopefully) make the right choice for you. Oh, and don't mistake sexual orientation and gender identity. They're more separate than I thought.