Since she really prefers certain locations to pee and poop, have you tried putting extra litter boxes in those locations? Maybe it is the location she likes and it has nothing to do with litter type, etc.
At minimum, it might make things easier on you. If it works she will get used to going in the boxes because of their location and maybe in a few months, after she is in the habit of using the boxes in her favorite locations, you can atttempt to slowly move the boxes to a location of your choosing.
Sometimes we have to adjust to the kitty's preferences.
Or, this may sound weird but ... Since she likes your neighbors pebbles, get some of the same pebbles and put some over the litter in her boxes.
Good luck.
Cat selectively uses litterbox! Help!
Re: Cat selectively uses litterbox! Help!
i think talking to the vet is a good first step. it is probably a stress thing tho, the bf's brother treating her like that may have made things worse, and even tho she likes your bf at times, she may be afraid of him, especially if other men have abused her. you should talk to him to be sure he is not discipling her for going on the carpet. that is definitely a guy response (one of the few things i have ever disagreed with my bf about was his response to the cat pooping on the floor) but shoving the cat's face in it or similar punishments make it all worse, because the peeing/pooping is in response to a health problem or stress in the home, so all you are doing is adding stress. the cat needs positive reinforcement, as well as making sure that she is healthy. you should discuss with the bf and make sure you are on the same page.