What are you using to clean the spots where she poops? And is it just poop or is she peeing outside the box too?
Sometimes, even thought we can't see or smell the poop/pee any more the kitten still can. And if it smells like someplace she went before then she will think it is okay to go there in the future.
Try getting a black light (they are actually pretty cheap) and running it over your carpet. It will show you if there is any residue that you can't see. If you can get that residue out and start all over will litter training (the crate is a good idea) it may help.
Behaviorists can be very good with certain problems, they are not a cure all and they are very expensive. I would try using the black light and cat attrak litter first.

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