Is she eating regular food? If so you have half the battle won. I prefer premium foods for my cats and dog so I have to go to special petfood stores for them, not the grocery store. Some very good names out there are Eagle Pack, Wellness. I like to look for foods that are made with holistic ingredients and human grade products.
I don't know of any litter that won't eventually mess up the works flushing it so even if it states flushable, I would not flush it. I use a product called Swheat scoop, it is made out of the outer husks of wheat so is perfectly safe if little tiger lilly accidentally eats some. It clumps fine and is also an earth friendly product.
Their eyes are usually a deep blue when very young. They will eventually turn color. I suspect mama cat may have been moving her babies and dropped this one and got spooked and did not go back for her. Thank you for taking her in.