Judging from the fight scene between Yuki and Ryoko in the Anime, the amount of blood she emits would lead me to believe that most or all of her is organic. (and the blood is red. Not some weird color like maybe hydrolic fluid color or anything. So it's normal blood that you see)
Her actual consciousness is probably not in the 4 dimensions as we know it, so the body is a normal human girl for intensive purposes. She simply manipulates her body in the same way she does the environment. If she needs to move fast she changes her body to move faster. If she wanted to fly, she could modify her body mass or directly change the gravity around her. But when she isn't doing anything special, her body is just that of a normal girl.
To further expand this, if you managed to "clone" Yuki's body through normal genetic science like nicking a piece of hair from her (that is, if she let you sample her DNA, would be hard to do this if she resisted
), that Yuki clone would grow up to be a normal human because it doesn't have a trans-dimensional consciousness controlling it.
If her consciousness was anything near that of a normal humen, she would have died from the first blow from Ryoko. But as you can see she doesn't really need her body to "exist".
How Ryoko was killed was not physical in nature. Her body literally dematerialized and what actually happened to her consciousness isn't known. Unless someone remembers the novels better then me and say for sure that she was actually "dead" for all intensive purposes. Also note that while her body was dematerializing she was able to still speak. In fact she showed no (outward) signs of cognitive depletion as thus her speech was not slurred or distorted from the process. Which might show that she never actually "died". Just removed from the planet/galaxy/dimension. Who's to say she can't come back? Ya never know!
That's my theory anyway.