Kilz works on slabs because it forms a barrier. If you are over a basement or on a raised foundation, some of the urine may have penetrated to the subfloor. Also, it may have gotten behind the baseboards and in the gaps between the wood floor and the wall. You will have to pull the flooring up anywhere the urine has gotten to the subfloor. The subfloor may also have to be patched.
Water and urine can soak into a wood floor to the extent that sanding will not be enough to get to clean wood. Be prepared to do a lot of patching if that's the case. If you can get the smell out but not the stains, refinish the floor in a dark color to help hide the stain.
I have not found Nature's Miracle to be of much use,