Make sure you clean the wood, once you remove the old carpet, with an enzymatic cleaner, so the stuff we humans cannot smell that mark a spot as "good spot to pee" will be removed.

Try playing a lot with Cookie - fishing pole-type toys so he can practice hunting, and other games he likes, to get him tired out. You may even want to try taking him on walks using a leash and harness, anything that will tire him out. Give him things to hunt that are NOT Baby Kitty. And maybe your mother, instead of adopting a new cat, can concentrate on building up Baby Kitty's confidence, so she will not act so much like prey, and won;t tempt Cookie to attack her. I would certainly not add another cat into the mix before getting the situation with these two figured out!