Hey man,
I just want to say, I know how you feel.
I don´t perceive myself as female, but I do still think parts of me are female, which gives me an equal amount of unease.
I take it you´ve had top surgery. As for bottom dysphoria I wear like three boxers with a packer so I don´t have to feel much of what´s going on and the bulge is natural, so people don´t start wondering why there´s nothing there.
The thing with intimacy, I´m pretty much in the same boat. And I think a lot of transmen are. I have no answer to that though.
Edited to add: if the unease gets real bad, you could discuss medication options with your GP. Some medication helps when the anxiety gets out of control.