People think because it kills something that's alive, it must be bad for all life, but glyphosate specifically targets an enzyme that only plants have.  

(She lived there when I bought it).We did several cleanings with an enzyme cleaner (Nature's Miracle) which helped but did not entirely eliminate the odor.

Have you looked at using an enzyme based cleaner?

I used an enzyme cleaner down there called Mister Icky Poo

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.