Is she just pooping outside the box? What brand of urine destroyer are you using?
I have a mobile baby and 5 cats, so I understand where you coming from. There are FAQs at the top of the board; try some of the suggestions there.
My 2 cents:
Pooping out of the box can be a sign your cat is anxious. We did not start having issues until DS started crawling. 2 of my cats are on antidepressants, and we are all happier.
I would also make sure you have 2 boxes. Some cats don't like to pee and poop in the same one.
Also, remember that she has gone through a lot of changes recently, and babies freak most cats out. Only one of mine will actually come up to DS and lay by him. DS just pet (with my help and supervision of course) another one for the first time. If he crawls toward them, they run away. It also wouldn't hurt to talk to a vet. I would add some cat trees, too. Cats like to be up high.