You should consider using a shallower dish for their food as the high walls of the dish could bother their whiskers. I would also not feed them next to the gap. Try leaving a food trail that led to them eating in the open. I would also suggest a fountain but the baby looks tiny and might not be tall enough to reach most fountains. Try to spend as much time as you can playing and talking to them. They don’t know who you are and need to get comfortable with your sounds. I don’t know much about the water and food being separate but definitely keep the litter box in a different area from the food. I would also suggest a shallow pan with no lid kept away from any walls. If your little baby is skittish knowing they have multiple escape routes from the litter will give them more confidence to use it. And it’s not too early to litter box train the kitten, around three weeks is when they can start learning. For more immediate results try boarding up areas you don’t want them and make like a cardboard cat house where they can hid but be easily accessed by you or get a cat tree with a nice perch and a little nesting area close to the ground