To me it sounds like you are trying the right things so I can't suggest anything else. Have you tried using soil/compost as litter? Some cats prefer it but seeing as she has never been outside I can't see why she would be more used to soil than normal cat litter.
Do you have a good vet that could give you some behavioural advice? Also has she generally been checked over by your vet? One of my cats had toileting problems due to stress, fortunately she didn't have cystitis or anything (got that checked) but it was all down to stress/behavious. The vets gave me some tips (extra tray, kalm aid and I already had feliway). If your vets are good maybe they could help brainstorm ideas with you.
I'm not too sure myself what else you could do, maybe some of the other may have some other suggestions.
I can imagine the current situation isn't great for you or your new addition because she is a bit restricted at the minute *hug*