A common problem with home urine removal is that people don't soak the soiled area as thoroughly as the original urine soaked it.

Another big one is the soil report.

Send me photos of what is underneath and I can label the type and tell you if it will pass as is.There are lenders who will do it without the permit but will cost more than a Fannie or Freddie loan.

The soil has been tested and it's ok.  

Pulling up that carpet in just the corners in various places shows that very nice hardwoods are underneath that carpet - including the stairs and bedrooms.

@Harjeet Bhatti Is a Gift of Equity eligible on a property that has apartments and commercial underneath?

The joists are all wood underneath, does that mean modular?

The list for new builds can be a lot trickier (poor construction/ construction defects, new materials being used that haven't stood the test of time yet, foundation issues from expansive soils or bad concrete being used (harder to know because the damage isn't visible yet), sewer line might be already jacked up or done wrong, windows or roof may not have been flashed properly but water damage isn't visible yet (I've seen new builds where you could literally see daylight coming in through gaps around the windows), grading or drainage issues, truss rise, nail pops, water intrusion, cheap appliances only made to last a few years or poorly installed, dirty ducts from registers not being covered during construction, wood shrinkage cracking the sheetrock, doorframes off/sticking doors and windows, apparently mold and meth may be present already... both old and new require due diligence and an experienced inspector. 

Our strategy would be to live in the property until we have our legs underneath and then slowly expand into more properties in the area/region.

One way would be to create a Series LLC that has child LLCs underneath it and having Land Trusts underneath each child LLC.