They have had romane, so I'll stick with that for now. They are still on the middle level and it looks like nothing has been touched on the bottom.
I've run into another issue. They were reliably using a litter box at the foster, but haven't touched it here. There is poop and pee all over this morning. Do I go in and clean everything or just let it ride the next 2 days? Also I put rugs down in there because everyone was freaking out about the vinyl, do you think I should pull them until they start using the litter reliably.
Can you post some picture of how it looks now?
Firstly, I would put them into a transportation box or what you have there and would clean the area using vinegar for neutralising urine smell as they like peeing in the same spot where the smell already, so I would put paper towel soaked in urine under their litter in the litter box and generous amount of poos too, so only litter box has urine and poo smell and everywhere else is clean and no urine smell.
Secondly, I would put their toilet box on the floor, say in the left corner and would fix some hay over it, also I'd place their water bottle and food bowl over or near, so they have everything around their box.
And when you bring them back from their transportation box put them directly into their toilet box which will only smell like them as you've cleaned around already.
Then leave them alone for a few hours or over night, then let us know how it was.
I don't see what rugs you have there, photo would be nice.
Don't get scared I think they just can't find their toilet maybe if you put their pee & poo into it and will make it easy to reach for them they will start using it.