Confining your cat adds stress to your cat's life, and, as you know by now, stress can lead to illegal toileting. Confinement can be a necessary tool in your cat's journey back to her litter box, but it should be used as a last resort, and after you have tried all of the other things first.
Run through this checklist to make sure you've tried it all!
Have you:
Ruled out any health issues?
Made sure your litter boxes comply with cat rules (they are hoodless, liner-free, clean, have multiple points of exit and entry?)
Made sure you have enough litter boxes? (your litter box count is equal to or greater than the number of cats you have +1)
Made sure you have a litter box on each level of your home?
Made a (huge) effort to cat-i-fy your home? (you have high up spaces, a variety of scratching options, a space where your cat can be away from dogs and kids)
Begun to spend a good 15+ mins of time with your cat each day, either playing or just chilling?
Spread your cat's scent around the house? (with more cat beds, face scratchers, extra brushing in new locations)
Increased your cat's hydration by re-evaluating his diet and adding water sources that are not next to his food bowl?
Tried to create a new association with the illegal toileting spots?
Attempted to deter your cat from urinating in the illegal toileting spots? (but never with punishment, spray bottles, shock pads, or yelling. See this for some respectful deterrents.)
Been patient? Change takes time, especially when it comes to cats. If your cat has made some progress after these changes but still isn't at 100%, then you might just need more time, or a few more changes.
If you've done all these things, and your cat is still not using her box, it might be time for minimal confinement. Not sure? Feel free to shoot me a message.