Former Stray, inconsistent litterbox use

This summer, I took in a stray cat who, most likely, had never seen a litterbox before. She spent her first month with me quarantined in my study and, during that time, I was able to get her to the point where she was using the litterbox 90% of the time. But since she's had the run of the house she's become more unreliable. I initially thought this was because she was getting disoriented in unfamiliar parts of the house, but by now she has completely settled in--and it's a very small house to begin with. I have tried to introduce her to the first floor litterbox with no success. I've even tried leaving the cover (it is enclosed) off and that does not seem to make a difference. I don't think it's a problem sharing a litterbox with my other cat, given that they both use the upstairs litterbox. I have tried placing her in the box after meals or after I see her peeing somewhere else and this hasn't helped (it did work with getting her to use the upstairs box). I have also tried spraying her favorite alternative spots with felaway and/or Nature's Miracle No Spray and they do prevent a return to that spot. But, unless I want to saturate my entire house in these, I haven't found a way of keeping her from just choosing a new spot. Any advice would be welcome.

Edit/update: I tried confining her to the bathroom with the litterbox. Unfortunately, she can open the door.