(still laying only 1-3 a day).
I'm confused by that. Is she laying between 1 and 3 eggs each day or one egg every three days? Or maybe something else.
I'm wondering if need to lower them to the floor or at least closer to the floor or hope if another starts laying she will go in?
There is nothing wrong with those nests, either how they are made or the height. People have been using nests like that for a long long time. If you want, you can modify some or provide other nests but you get no guarantee that it will change anything.
Chickens are living animals, they will do what they want. Sometimes we can influence them but it does not always work. So what can you do?
It sounds like she has made her nest where she wants it. How bad of a place is that? Is she OK continuing to lay there? If you are OK with that, what is your problem?
You might try building a nest and putting it in that spot. If that makes the spot OK, good. If not, try moving that nest a foot or so toward your main nests every 3 or 4 days after she gets used to using it. This does not always work but a lot of the time she will follow the nest. When you get her back to the area of your main nests and she is used to that area, remove the nest and see if she uses one of yours.
You can modify one of your nests so you can lock a hen in there. Then when you catch her on her nest laying an egg catch her and lock her in the real nest until she lays that egg. That may mean chasing her down with a net. This is what I do but I'm retired so I can catch her on her nest when she is laying. Usually I only have to do this once and she makes the switch.
Some people say they have had success by blocking off the area where she is laying to force her to find a new nest. I've never had any luck trying that, she just lays next to whatever I put there.
My nests are available well before they start to lay and I use fake eggs. I have hens that are laying in those nests so the pullets have someone to show them where to lay. You don't have that yet but the vast majority of my pullets start laying in the real nests. It will get better for you.
They face the back wall so (to me ) they are dark inside and even when the door is open when they are in the run they seem in the dark to me but maybe they are not dark enough? Or do I need to remove them and go with like milk crates or litter buckets instead? Here's pics of the current nesting boxes (pic 3 is with the flash pic 4 is without flash to show how dark during the day) last pic is where she has been laying behind roosting bar.