James, congratulations on your new baby. However, the introduction to Pete should not have taken place until your little gal had her stitches out. She's already STRESSED out with everything that has gone on -- surgery, leaving the breeder, coming into a new home with a new cat smell. It can be overwhelming. I know it takes patience to keep these two apart, but this little lady does not need any additional stress right now. She needs to heal from the surgery. The onesies that they now use -- is easier on them than the cone. And it may be hot and uncomfortable, but the stitches need to be left alone until the incision heals. Plain and simple. Personally, I would have asked the breeder to keep her for another week -- only so that you didn't have to deal with all of this.
However, she is now with you and she has met Pete, so things are what they are. She needs to be monitored as much as possible and she needs to be as cool as possible. Tile and wood floors are cooler than carpet. If you don't have air conditioning, then a fan would help. Know that this is just for several days.
As for using the litter box, it is very common for a new kitty to not use the litters for 48 hours or so. It's the stress causing this. Be patient -- she will use it.
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