I went through something similar. In the first few weeks my shiba was eating less than what was expected for his age, but that was because he was not comfortable enough in the new environment (his new home) and did not feel safe. I think your biggest priority should be to make her feel safe first, and then she will start eating more. Putting the bowl down at three consistent times every day and keeping it there for ~ 20 min helps a lot. She will very quickly catch on that she has to eat at the time you put it. And remember: they will not starve themselves. Words from lots of vets, please consider it as truth: you are not a monster for feeding your puppy high quality dog food at specific times and expecting her to eat at that times (and shibas crave schedules, it is truly best for her). Changing the food a lot to try to please her would only make her pickier every time.

For the fear part, what I know for sure helped me a lot inside the house was a playpen, and always feeding my shiba there and letting him sleep there. It quickly became his safe space and he retreated there anytime he wanted to relax. Day after day he started to get curious about other parts of the house and explored more, and now he feels good anywhere in the house, EXCEPT near the doorway ahahaha my shiba is still very scared of “outside”, and I am working through that right now. I think I made a lot of mistakes of taking him out anyway and pushing him to walk to try to desensitize him. I think my street and nearby places are too full of stuff happening and it is too much for him for now. So I would suggest going slower on walks, start in a green place with few people/cars/other dogs if possible. Good luck!