Thank you for adopting a kitten from a shelter! She is still very young at 9 weeks old, and you don’t know the circumstances of her birth and how she was raised so this is probably why she is acting afraid. It will just take lots of PATIENCE on your part to bring her around to trusting you. I would feed her wet food and maybe offer it to her from a spoon that she can lick while you are holding it, so she knows that her food comes from you. You can also get some goat’s milk (warmed in the microwave) that would be good for her since it has probiotics and will help keep her hydrated and will help with her intestinal issues. She should see a vet to rule out parasites (worms) and for a general check up and her first vaccinations.
Wand toys that you can dangle in front of her to play with will help to socialize her. Most kittens need socialization from the time of birth (or around 2 weeks after) to 5 weeks old. Meaning lots of handling, petting, even if they have moms that are there to feed and raise them. All of my cats have been hand reared and have been handled since birth so I have never had the problem of them being afraid of humans. Some kittens have been from feral moms and if the mom acts afraid, then the kittens do too. Just lots of time and patience on your part will go a long way.
Also, put her food and water where she knows where they are, and her litter box (not right next to) but close where she knows where it is in proximity to her food and the rest of the house. Remember, she is just a baby and has to learn to use the litter. Also, cats do not like strong smelling litter, so unscented is best to get her to used it. Keep an eye on her after she has been up for a while, and then place her in the box, to prompt her to use it.