With that much of a pet urine issue you will almost certainly lose the hardwood and possibly areas of the sub floor.
We did a house in Poughkeepsie, NY that the owner had died in and had like 15 cats running around. We actually went down to the sub floor in the whole house and still had to cut several areas of sub floor out before getting the smell out of there.
Keep in mind that you may also have issues with the smell sticking to the ceiling and walls. A good wipe down with soapy water should be able to take care of all of that. That will also be true for all the trim work and doors. Basicly all surfaces.
I have also found that cats, being the nasty little buggers they are, love to do their buisness in and around radiators, furnaces and anything giving off radiant heat. Be sure to check those areas.
Disposing of any cats that may be creeping around will probably help also, which by the time you get done with this project your gonna hate cats for the rest of your life.