Hey there, and welcome to the forum!
To answer your questions, the best way to get the eyes you want is to send them a high definition picture of the character you are trying to emulate. The eyes are printed on a piece of plastic and set inside the head, which means they can get the eye shape pretty much exactly like you want. Try to get a picture of the front of the face, just to make it as accurate as possible. You can ask any anime owner here, and they will happily oblige if you want to see examples of eye shapes. BD also has lots of choices too, but they're all quite similar and may not be what you would like. Hunt around for your preference.
As far as skintone, you can pick from regular and tan, and pink. Tan isn't super dark, though.
As far as storage goes, yes, she comes in a fairly small box with her head detached, but I wouldn't recommend storing her that way. She comes curled upin a little ball, and I'm sure it wouldn't be healthy for her joints. While you can take her head off easily, doing that repeatedly would wear out the socket. My girl just sits on a little shelf in the closet, and I have a keyed lock on the doorknob. However, I have also considered this and you can try it: you can purchase clothing keepers for storing suits that hang in the closet. They are bigeenough to hide shapes inside, and usually have a small place for a padlock to keep people from prying. I would loop a rope under her arms for support and hang her from the bar in the keeper, then hang the whole thing up and padlock it. It should work, unless you have someone who regularly raids your closet.
