Those toilets are pricey, but nice.The OP probably could replace the valves underneath instead of replacing the whole toilet.

To fix that I would have had to either rip up the whole bottom floor of my house, go underneath and jack them up, or double up the floor joists.

There is no question that it was affected by the nationwide downturn three years after opening but what a great project:Atlantic Station is located on the site of the Atlantic Steel mill, which opened in 1901.[1] The steel mill was nearly closed in the mid-1970s, but it remained nominally operational primarily to avoid the huge costs it would have required to remediate the soil contamination present after years of operation.[2]Developer Jim Jacoby, who also redeveloped Florida's Marineland, began putting the project together in 1997 when his company became the property contractor of the land.

Since it would be difficult to place, (well mostly remove spacers) from underneath the sheet rock, I was hoping to just align my first row and all edges with the vertical edge of the sheet rock, then have the 5/8" base molding placed over flooring. 

What is underneath it that caused it to be raised in the first place?

The window on underneath the stairs is a ~200 sq ft storage room with bathroom.

The "Goo" then hardens and keeps the slab at height (for a while), because it's tree roots and soil conditions that make the cement move.Sometimes they drill hole to inject it, sometimes they come at it from the side.It's FAST..you can look it up on the web (see YouTube).For the Mockups I use GIMP....it's like Photoshop with less features, but enough to get the job done.There is a learning curve to it.

Have you posted an ad online for free soil?

If it is particle board I would replace it.Here is a technique for getting rid of the oder for good,Remove carpeting, padding and other flooring around the areas you suspect urine has leaked into the subfloor.Apply an enzymatic pet cleaner (like Nature's Miracle) to the soiled areas and allow them to dry thoroughly for 24 to 48 hours.

Yeah I have a friend in army with 706 credit so I don't have to rely on parents credit and from looking at the house its just cosmetic needs like paint carpet and maybe a little modern updates but everyone once you start taking things apart there maybe some other damaged underneath but from the look I think 10,000 in repairs would do the job.