It sounds like you're being about as good a friend as you possibly can. Feel free to be honest that she's making you uncomfortable. If one of your other female friends was just a good friend to you and you didn't see any possibility of a relationship with her, you would be a little uncomfortable with her flirting with you and trying to cuddle up with you. And no matter what your relationship status, it's pretty inappropriate for a woman to come to a man and start asking his opinion about her crotch.
I think she's more confused by your relationship than you are. You're friends, and she's going to ruin that friendship if she behaves in some bizarre sexual manner around you.
If she's only recently started taking hormones, though, she's going to be a little flaky. It's like all your emotions are amplified and you can experience levels of attachment, loneliness and resentment that you never had before. It can be overwhelming.
Like Ila said, it would help her to find other trans women to talk to about stuff and not harrass her best friend with uncomfortable questions about her cock. I mean, OMFG.
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