A layer of 5/8" type-x drywall on the ceiling and min. 1/2" drywall around structures ( garage walls) supporting the partition would be required. 

Plumbing: I would plumb the units with Pex supply lines because they are much more likely not to burst if they freeze.

With houses being different, even if all the supplies are the same, a larger bid can be a bit of guess work on everyone's part sometimes leading to vastly different amounts that place Contractor A much higher than Contractor B where the next job may have them flipping the other way.

In an A class neighborhood, the land value is greater and you would have the option to build bigger and better than what was there previously because of the average price per sqft in the immediate vicinity and high demand (combined with low supply) from homeowners in the area, would allow the new bigger/better property to appraise. 

Even though in some places one organization collects taxes for multiple taxing jurisdictions....for example the county may collect for, the county, the city, the school district, the hospital district, the community college district, the water supply, the noxious weed control district, etc, the individual entities may have lists too they would give you.   

Any recommendations for the best structural engineers in Indiana?

Likewise, I created an entire post on how to properly structure your deal if you purchased with cash. 

How on earth would someone structure something like this?

. - White goods are usually a tenant's responsibility- Most repairs are a tenant's responsibility with major structural issues being the owner's responsibility.

The Trust is not for asset protection, however the overall structure of Trust and LLC mitigates the down side (not just the risks).