As you said, any new name sounds odd, so until you start using it anything is going to be weird. No one in real life calls me Alex (I've just realised that I've never been called Alex aloud which kind of freaks me out), but my ex used to call me Adam because it was the name I'd originally chosen, so sometimes that feels more right to me. I know though that Alexander is better for me in the long run though because of how I tried to get people to call me that when I was a kid and I'm not like any of the Adam's I know at all, but I am like an Alex I know.
Do you know what name you would have been called if you were born male? It sounds like you want to honour your mother's wishes and like for biblical names.
Out of the three you've put there Jeffrey/Jeff seems to fit what I've seen of you on here more, I know a couple of Jacobs and Joshuas and they've all been quite reckless, and a bit... lacking... in the intelligence department, whereas you seem more measured and controlled. That said, I don't know any older Jacobs or Joshuas, and the only Jeffrey I know of is a character in a TV program.
I can sort of sympathise with wanting a completely male name, I'm calling myself Alexander more at the moment because of my dysphoria, and did contemplate changing it because people pointed out that having an androgynous name might hinder my passing, but I feel that when people know my chosen last name their brains will automatically think 'male' anyway because it contains a male name.