Thank you everyone who took the time to answer and offer their advice.
We replaced the old carpeting with Pergo floors and took all the recommended precautions when installing this stuff.

We also took the cat to the vet to rule out any health problems.
The vet believes she is having a difficult time adapting to the new house...but we are making some changes (including adding a litter box to this level instead of just one in the basement). We have one of those litter boxes that automatically disposes after the use so she has "clean" litter.

So again thank you for all your advice and we will stay in touch and provide updates of the cats as we settle in.