Here's an article about introducing cats and dogs: http://www.thecatsite.com/Behavior/5...s-to-Dogs.html
Sounds like kitties and puppy may need to be separated for a while.
She may have a UTI from the stress, so I agree with White Cat Lover - a trip to the vet is in order to make sure it isn't that.
Also, you definitely need to purchase a black light to go through your house to find every place she has peed. It will turn up as an orange splotch in the black light.
Any place she has soiled MUST be completely cleaned with an enzyme cleaner. Nature's Miracle is an example of one, and it is available at most supermarkets or pet stores. We use Nok-Out (http://www.nokout.com
), and you may want to use Anti-Icky Poo. I suggest this because you may also want to consider Calm and Serene or Rescue Remedy Flower Essences - all available at the same site: http://www.catfaeries.com
. Flower Essences help some cats, not others. I'd also purchase Feliway spray - it helps most cats feel calmer in a stressed environment, and it, too, is available at catfaeries.
Anyway, if you haven't used an enzyme cleaner and it's gotten onto/into the laundry basket or the bathroom carpet, or any carpet &etc, it may smell clean to you, but it doesn't to kitty. You have to use a lot of it on carpeting - and unfortunately, your clean clothes soiled by kitty need to be first washed with the enzyme cleaner and then washed like regular laundry. Same with any throw rugs.
You may also want to consider all of the above AND try purchasing Cat Attract Litter. If your kitty isn't ill, but is just stressed, you really need to help reduce her stress with the above suggestions, giving her more attention, some dog-free time, and the Cat Attract Litter has been helping a lot of cats, so it might be worth a try to - but only in combination with stress-reducers for kitty.