Thanks for the replies! I did hear about feliway, and may try it, but she sleeps on the bed with us with the other cat and spends a lot of her time sleeping on our laps, so definitely no lack of cuddles.
She is also very curious and inquisitive all the time, and already bosses the older cat around a bit with enforced playtime, along with clawing the dog's paws (they have a strange paw tapping game with her under the couch and him in front of it), so she *seems* happy at least.
Next week we have a vet appointment for her second set of shots, so I will ask then. I'm not quite sure how to get a urine sample of her, I once had to get one of my dog, and that was difficult enough, lol!
She does use the litter to poop, so not sure if she dislikes the box or litter, she is in there every day and we clean it every day.
The problem is that the smell is terrible, adn I can't afford to buy new couches and mattresses to get rid of the smell, and not sure if the cleaners I used are effective in making it smell-neutral to cats. If she thinks that is her place to pee, I don't know what to do about it. Sigh.