Yeah, women are nutty. I can say that despite my own XX chromosomes; whenever I interact with NT women, they make less sense to me than NT men (though only marginally less, in the case of jock-type men). Men seem more straightforward to me. But nerdy NT women make sense to me just like nerdy NT men do, so it's not like all of them are that cryptic. I think maybe women tend to be more socially elaborate; or at least, some women are, or at least they're culturally encouraged toward social complexity. Wherever the difference comes from, I often find men easier to read--but not all men are easier to communicate with, and not all women are harder to communicate with. Quite a few of my best friends have been female; about half, in fact.
It is much easier to just communicate in words. Ask her what she's feeling; don't assume. If she's a good enough friend, then tell her you suck at reading faces and you're going to have to ask her straight out what she's feeling so you'll understand. If a girl takes that the wrong way, then she's probably too picky and touchy to be a decent friend (or more-than-a-friend) to begin with.
It might help to try just "not noticing" that they are female. I don't mean pretend they're guys; I mean, just treat them like people-in-general, instead of freaking yourself out by always remembering that they're female. Yes, men and women are different (culturally more so than biologically), but the differences between individual people are much greater than the average difference between male and female. You have to get to know them as individuals. Maybe that takes you longer than most people, but so what? Some things in life will always be tough to do. That doesn't mean they aren't worth it.