Ozone in sufficient quantity is supposed to be very effective at removing odors and killing mold.another cheaper option might be the enzyme odor eater stuff they sell in pet stores - I remember it being very effective on an expensive couch my parents had that a cat peed on..it's a clear liquid

Or DIY, you can use "Natures miracle" spray which is sold at retail stores which is an enzyme based cleaner that works great on urine and will break down the ammonia (and strong associated urine smell) in urine that makes it pungent.

We did what @Ryan Ingram suggested and ran an Ozone machine for a few days, in conjunction with scrubbing the ever-loving-you-know-what out of the floors with an enzyme based cleaner that's made for urine smells.

It was overwhelming and I tried every product (with enzymes, etc).

The research I did pointed heavily toward enzymes and shellac as the best solutions for penetrated odors like this.

(Cheap way in place of nature's eradactor) as I've read that the enzymes in PERISIL effectively kill all life stages (contract killer) but still Im seriously so close to becoming insane its really bad how much it has affected my mind.

I'm feeling pretty confident about charging for all the labor and materials for the entryway but I am not sure what to do about the carpet.Should I itemize all my costs including my time and the enzyme treatment that didn't work even though I am waiving those costs?

I have seen carpet with odor that can't be removed even with the fanciest enzyme cleaners. 

They make special pet urine cleaners that's suppose to have enzymes that dissolve the urine smells.

We'll plan to treat the floor with some type of enzyme that kills bacteria, but I'm also planning to run an ozone machine.Do you have any recommendations of machines you've used and for how long to run them?