As per the permits I am sure we will need to file with the bathrooms, walls, and backyard fence.

Well- filing your taxes incorrectly isn't really allowed. 

Joe -- my point was there is no authoritative guidance that supports the position of your CPAs.Don't worry about whether failure-to-file a 1099 makes a payment non-deductible. 

I've done a bunch of mortgages for the formerly incarcerated; we don't document it anywhere in the loan file (so there's no good stats on it), but they disclose it to me in the form of "hey Chris I have a record, I did [crime here], is that going to be a problem?"

However be mindful you are also required in this case to file an informational return, Form 5472.

After the CU report is completed, the report is then publically filed with the Miami Dade clerk of courts. 

Or just fill Schedule E while we file joint return? 

The dark gas station owner files bankruptcy and has no money for you to go after to make them clean up the contamination of their property and your property.If a seller is smart they will not sign such an agreement that they would be responsible for further testing (a phase 2) and further would be responsible for the clean up etc.

We found it on public records because the seller had an NOD filed against it.

You would have ongoing filing requirements with the State and would need to keep business records and documentation.You also want to look at whether a pass-through entity helps your bottom line and your taxes.