Oh yes I know exactly what you're talking about. I was that way myself. I guess I still can be at times. It's natural, it really is. I mean you're going to read that and be like pfft I totally don't believe you, but it's natural. It's like a big thing in life and it can bring about huge changes and it's natural to doubt what you're feeling and it's also natural to be scared that maybe this isn't the right thing or that maybe you're making it all up in your head, but the fact is it's there and it is bugging you. That's how it comes off to me anyways, and that is exactly how I felt before I started my HRT last month.
Don't push yourself though, you have to take time to think everything through. It may be your best chance at a happy life, but you still have to fully reach that conclusion, even if you still have some lingering doubts and fears. If you didn't I'd say there was something wrong, it's human nature to feel those things ESPECIALLY about huge life decisions like this. Don't worry though, despite all the self doubts and wondering if you're making it all up you are not alone.
I too had wondered similar things if not the same exact things as you. the whole " revolves around the fact that I didn't recognise these feelings for so long that maybe they're not real" and I've had people question me on exactly that. Like saying stuff like, "Well you never said anything before, why now??" For me, at least, I knew something was off about myself but because I didn't know what it was, what was causing it and why I just thought it was completely normal. But now I know, and I was able to identify years of self doubt and self loathing and all that I'm able to say something.
Find someone to talk to, I mean it doesn't have to be a therapist but reach out to someone and talk it through with them, that might help you out. Be sure they are willing to listen and if they don't know much about your situation be prepared for some weird and awkward questions, and be willing to try and at least answer them best you can. It will help you work through it trust me.