The floor area of the cage is not too bad, although longer would be better - eg 100cm x 50cm. The main issue is the height is quite tall and there can be fall risks then. So really if it was shorter but wider it would be much better

That also means they have more floor area for nesting and roaming. It's nice to have one level - eg a platform or shelf, that isn't too high, as it's good for them to have somewhere else to go and a solid shelf or platform to put heavier items on, eg a sand bath.
She has lots of lovely deep bedding there

I think a slightly larger house would help as well, at floor level - or a shoebox house, which you can make quite easily, and that's then big enough to put a corner litter tray inside. If you give them a large house, they almost always use a corner of that as a toilet inside and will use a litter tray if you put it there. Then it's very easy - you just lift the roof of the house and empty the litter tray every few days. It seems to be a natural instinct to want their toilet not to far from their nest and ideally ensuite!
To make a shoebox house you just cut the base of the shoebox out and keep the lid as a lift off roof, then cut a hole for a door - it's best to have the door on one of the long sides, near one end, as then the other end is darker inside. The almost always choose to nest at the dark end and use the toilet at the less dark end, so then you could put a corner litter tray, with sand in, at the back corner of the door end.
If you put something like a bendy stick bridge over the door as well, then it makes it even darker inside and the tunnel entrance tempts them in - she would probably move in the first night, if you remove the old house at the same time.
There are things you could do to make the height of the current cage safer, but I would look to upgrading it to something with more floor area and less height.
I couldn't see a 3 tier pawhut on Amazon. Are you in the US or the UK or elsewhere?

It makes a difference because tanks are much cheaper in the US but in the UK and Europe there are quite a lot of alternatives to glass tanks.
Looking at the photos, for now I would probably remove the left hand shelf and ladder and put the shoebox house (or similar) there. And lower the right hand shelf so it's not too high. This will still leave quite a drop if she happens to climb the bars at night or monkey bar across the roof and drop (we often don't see these behaviours as they can be when they're at their most active at night).
The other option is to put both shelves at the same height somewhere between the height of the left and right ones, and use the ladders to sit across them so there's just a hole in the middle, then have access to those via either another ladder or tube going up through the hole - but then you'd need something like a large hide sitting over the hole so she couldn't fall right from the top through the hole. This effectively makes a "full level" so breaks up the height. It's quite hard to make a very tall cage safe.
Another option to effectively reduce the height is make the base deeper by putting cardboard or perspex inside the bars and having double the height of the bedding and just one shelf. So effectively then you'd have a very deep base with deep bedding and less height above the bedding. If that makes sense!